Variant report

Variant	rs915943
Chromosome Location	chrX:153627496-153627497
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chrX:153627189-153627541	GM12878	blood:	n/a	n/a
2	CHD1	chrX:153626608-153628530	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chrX:153625570-153630890	GM12892	blood:	n/a	n/a
4	MAFF	chrX:153626674-153627691	K562	blood:	n/a	n/a
5	BCLAF1	chrX:153626311-153627529	GM12878	blood:	n/a	chrX:153627240-153627253
6	MAZ	chrX:153625300-153628574	IMR90	lung:	n/a	chrX:153627312-153627323 chrX:153627313-153627322 chrX:153627199-153627208 chrX:153627314-153627321 chrX:153627312-153627323 chrX:153627313-153627322 chrX:153627313-153627323
7	POLR2A	chrX:153625239-153628974	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chrX:153625335-153631207	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chrX:153625822-153628694	HEK293	kidney:	n/a	n/a
10	MAX	chrX:153625679-153627668	MCF-7	breast:	n/a	chrX:153627312-153627323 chrX:153627313-153627322 chrX:153627199-153627208 chrX:153627313-153627323 chrX:153627314-153627321 chrX:153627312-153627323 chrX:153627313-153627322 chrX:153627313-153627323
11	KAP1	chrX:153626081-153627744	U2OS	brain:	n/a	n/a
12	POLR2A	chrX:153625646-153631123	Hela-S3	cervix:	n/a	n/a
13	BCL3	chrX:153626271-153627766	A549	lung:	n/a	chrX:153627240-153627253
14	GATA3	chrX:153625454-153627519	A549	lung:	n/a	n/a
15	USF2	chrX:153626282-153628625	Hela-S3	cervix:	n/a	chrX:153627312-153627323
16	RELA	chrX:153625520-153627604	GM15510	blood:	n/a	n/a
17	MTA3	chrX:153625357-153628684	GM12878	blood:	n/a	n/a
18	POLR2A	chrX:153625722-153628835	K562	blood:	n/a	n/a
19	POLR2A	chrX:153625750-153627502	NB4	blood:	n/a	n/a
20	GTF2F1	chrX:153625936-153627824	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chrX:153627431-153627637	A549	lung:	n/a	n/a
22	POLR2A	chrX:153625340-153630862	HUVEC	blood vessel:	n/a	n/a
23	POU2F2	chrX:153627484-153628021	GM12891	blood:	n/a	n/a
24	TEAD4	chrX:153626241-153627769	K562	blood:	n/a	n/a
25	BCLAF1	chrX:153626406-153628888	K562	blood:	n/a	chrX:153627240-153627253
26	WRNIP1	chrX:153626558-153627831	GM12878	blood:	n/a	n/a
27	PML	chrX:153626195-153628084	K562	blood:	n/a	n/a
28	POLR2A	chrX:153625651-153631217	GM12892	blood:	n/a	n/a
29	ZNF143	chrX:153625939-153627516	K562	blood:	n/a	n/a
30	MAX	chrX:153625828-153627599	SK-N-SH	brain:	n/a	chrX:153627312-153627323 chrX:153627313-153627322 chrX:153627199-153627208 chrX:153627313-153627323 chrX:153627314-153627321 chrX:153627312-153627323 chrX:153627313-153627322 chrX:153627313-153627323
31	POLR2A	chrX:153625323-153627651	K562	blood:	n/a	n/a
32	MYC	chrX:153625702-153627520	NB4	blood:	n/a	chrX:153627312-153627323 chrX:153627313-153627322 chrX:153627199-153627208 chrX:153627313-153627323 chrX:153627314-153627321 chrX:153627312-153627323 chrX:153627313-153627322 chrX:153627313-153627323
33	USF1	chrX:153627120-153627500	ECC-1	luminal epithelium:	n/a	n/a
34	ARID3A	chrX:153626575-153627942	K562	blood:	n/a	n/a
35	SMC3	chrX:153626602-153627501	GM12878	blood:	n/a	n/a
36	POLR2A	chrX:153625672-153627745	GM18526	blood:	n/a	n/a
37	NFIC	chrX:153626179-153627612	GM12878	blood:	n/a	n/a
38	MXI1	chrX:153625493-153627555	HepG2	liver:	n/a	chrX:153627314-153627323
39	BCLAF1	chrX:153626391-153627697	K562	blood:	n/a	chrX:153627240-153627253
40	CCNT2	chrX:153625770-153627613	K562	blood:	n/a	n/a
41	CHD2	chrX:153626303-153627650	K562	blood:	n/a	n/a
42	POLR2A	chrX:153625845-153627683	U87	brain:	n/a	n/a
43	CREB1	chrX:153626245-153627531	GM12878	blood:	n/a	n/a
44	REST	chrX:153625420-153627555	H1-neurons	neurons:	n/a	n/a
45	POLR2A	chrX:153625333-153630712	K562	blood:	n/a	n/a
46	POLR2A	chrX:153625498-153631026	PFSK-1	brain:	n/a	n/a
47	MAX	chrX:153625792-153627636	NB4	blood:	n/a	chrX:153627312-153627323 chrX:153627313-153627322 chrX:153627199-153627208 chrX:153627313-153627323 chrX:153627314-153627321 chrX:153627312-153627323 chrX:153627313-153627322 chrX:153627313-153627323
48	MYC	chrX:153625882-153627770	MCF10A-Er-Src	breast:	n/a	chrX:153627312-153627323 chrX:153627313-153627322 chrX:153627199-153627208 chrX:153627313-153627323 chrX:153627314-153627321 chrX:153627312-153627323 chrX:153627313-153627322 chrX:153627313-153627323
49	POLR2A	chrX:153625308-153630689	HepG2	liver:	n/a	n/a
50	POLR2A	chrX:153625701-153629009	GM19193	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chrX:153284396..153286252-chrX:153625744..153627759,3	K562	blood:
2	chr15:44828896..44829631-chrX:153626751..153627511,2	HCT-116	colon:
3	chrX:153624383..153633652-chrX:153704408..153721325,48	MCF-7	breast:
4	chrX:153625463..153630462-chrX:153744222..153748220,7	K562	blood:
5	chrX:153580991..153583876-chrX:153626636..153628622,3	K562	blood:
6	X:153625659-153635385..X:153719993-153730954	GM12878	blood:
7	chrX:153624019..153633071-chrX:153652023..153663795,26	MCF-7	breast:
8	chrX:153625830..153633897-chrX:153767392..153772063,11	K562	blood:
9	chr2:74775602..74777340-chrX:153625659..153627602,2	MCF-7	breast:
10	chr14:69864750..69865963-chrX:153626613..153627599,3	Hela-S3	cervix:
11	chrX:153625623..153631615-chrX:153684928..153690706,13	K562	blood:
12	chrX:153625092..153628095-chrX:153742343..153746909,6	K562	blood:
13	chrX:153625525..153632382-chrX:153663983..153668753,13	K562	blood:
14	chrX:153624581..153628414-chrX:153743394..153746552,8	MCF-7	breast:
15	chrX:153236571..153238114-chrX:153626626..153628138,2	K562	blood:
16	chrX:153624113..153628937-chrX:153667362..153675322,17	MCF-7	breast:
17	chrX:153582162..153585045-chrX:153627001..153630604,4	K562	blood:
18	chrX:153625731..153628141-chrX:153991009..153993068,2	K562	blood:
19	X:153625659-153635385..X:154053104-154056925	GM12878	blood:
20	chrX:153361716..153363371-chrX:153626591..153628613,2	K562	blood:
21	chrX:153235275..153239304-chrX:153624971..153627980,7	K562	blood:
22	chrX:153594250..153603496-chrX:153624447..153635089,39	K562	blood:
23	chr22:41841590..41844551-chrX:153627454..153629001,2	MCF-7	breast:
24	chrX:153624542..153632362-chrX:153710560..153721332,23	K562	blood:
25	chrX:153553264..153555915-chrX:153626596..153629140,2	MCF-7	breast:
26	chrX:153625784..153628444-chrX:153721433..153724368,3	K562	blood:
27	chrX:153625296..153629968-chrX:153767983..153777827,13	K562	blood:
28	chrX:153592401..153602834-chrX:153624077..153632705,30	K562	blood:
29	chrX:153586062..153591083-chrX:153626549..153633665,7	K562	blood:
30	chrX:153589749..153593793-chrX:153626284..153628213,4	MCF-7	breast:
31	chrX:153626135..153631801-chrX:153703936..153709269,13	K562	blood:
32	chrX:153625254..153633054-chrX:153663966..153667311,10	MCF-7	breast:
33	chrX:153624567..153628166-chrX:153772694..153776749,9	K562	blood:
34	X:153625659-153635385..X:153657611-153671976	H1-hESC	embryonic stem cell:	embryo
35	chrX:153625628..153632278-chrX:153692369..153698999,8	K562	blood:
36	X:153625659-153635385..X:154119150-154130142	GM12878	blood:
37	X:153625659-153635385..X:154140465-154148278	K562	blood:
38	chrX:153192734..153195592-chrX:153625639..153627595,2	MCF-7	breast:
39	chrX:153586997..153589910-chrX:153626085..153628090,2	MCF-7	breast:
40	chrX:153625197..153632179-chrX:153731627..153740154,10	K562	blood:
41	chrX:153624545..153632466-chrX:153709449..153721332,27	K562	blood:
42	chrX:153625011..153628689-chrX:153675821..153678594,3	MCF-7	breast:
43	chrX:153625410..153630111-chrX:153684839..153690625,12	K562	blood:
44	chrX:153624619..153634737-chrX:153752670..153765167,48	K562	blood:
45	chrX:153626573..153628178-chrX:153978925..153981640,2	K562	blood:
46	chrX:153624391..153630513-chrX:153767458..153777755,28	MCF-7	breast:
47	chrX:153594620..153614384-chrX:153624179..153643019,157	MCF-7	breast:
48	chrX:153605609..153613633-chrX:153623295..153631024,31	K562	blood:
49	chrX:153625412..153631801-chrX:153757258..153764804,13	MCF-7	breast:
50	chrX:153625461..153628798-chrX:153677584..153681082,4	K562	blood:

Variant related genes	Relation type
RPL10	TF binding region
SNORA70	TF binding region
ENSG00000196924	Chromatin interaction
ENSG00000211524	Chromatin interaction
ENSG00000071859	Chromatin interaction
ENSG00000177854	Chromatin interaction
ENSG00000130826	Chromatin interaction
ENSG00000172534	Chromatin interaction
ENSG00000071889	Chromatin interaction
ENSG00000089820	Chromatin interaction
ENSG00000102119	Chromatin interaction
ENSG00000179523	Chromatin interaction
ENSG00000183864	Chromatin interaction
ENSG00000224069	Chromatin interaction
ENSG00000130827	Chromatin interaction
ENSG00000237859	Chromatin interaction
ENSG00000007350	Chromatin interaction
ENSG00000203879	Chromatin interaction
ENSG00000261773	Chromatin interaction
ENSG00000105968	Chromatin interaction
ENSG00000073009	Chromatin interaction
ENSG00000196976	Chromatin interaction
ENSG00000169057	Chromatin interaction
ENSG00000234183	Chromatin interaction
ENSG00000100632	Chromatin interaction
ENSG00000264484	Chromatin interaction
ENSG00000126903	Chromatin interaction
ENSG00000115318	Chromatin interaction
ENSG00000184216	Chromatin interaction
ENSG00000115325	Chromatin interaction
ENSG00000160219	Chromatin interaction
ENSG00000203870	Chromatin interaction
ENSG00000264783	Chromatin interaction
ENSG00000104131	Chromatin interaction
ENSG00000029364	Chromatin interaction
ENSG00000102178	Chromatin interaction
ENSG00000160211	Chromatin interaction
ENSG00000071553	Chromatin interaction
ENSG00000264631	Chromatin interaction
ENSG00000197180	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12007167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17426	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2070816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2070822	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2239470	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2872817	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs4446899	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs4898478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4898479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5945185	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs5945413	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs5945423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531227	chrX:152864376-153655730	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
2	esv33199	chrX:152864376-153820241	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	276 gene(s)	inside rSNPs	diseases
3	nsv528291	chrX:152864376-153827637	Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	277 gene(s)	inside rSNPs	diseases
4	nsv915605	chrX:153333946-153783638	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	204 gene(s)	inside rSNPs	diseases
5	nsv519042	chrX:153348431-153829693	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
6	nsv532962	chrX:153564946-153870337	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	199 gene(s)	inside rSNPs	diseases
7	nsv532963	chrX:153576890-153822717	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	195 gene(s)	inside rSNPs	diseases
8	nsv817569	chrX:153592317-153634020	Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
9	nsv530281	chrX:153622940-153783184	Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
10	nsv532964	chrX:153622940-153854307	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs915943	RPL10,SNORA70	cis	intralobular white matter	BrainEAC
rs915943	RPL10,SNORA70	cis	occipital cortex	BrainEAC
rs915943	RPL10,SNORA70	cis	hippocampus	BrainEAC
rs915943	RPL10,SNORA70	cis	frontal cortex	BrainEAC
rs915943	RPL10,SNORA70	cis	thalamus	BrainEAC
rs915943	RPL10,SNORA70	cis	brain	BrainEAC
rs915943	RPL10,SNORA70	cis	cerebellar cortex	BrainEAC
rs915943	RPL10,SNORA70	cis	temporal cortex	BrainEAC

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:153624800-153627600	Active TSS	Pancreas	Pancrea
2	chrX:153624800-153630000	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
3	chrX:153625200-153627600	Active TSS	Liver	Liver
4	chrX:153625200-153627800	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chrX:153625200-153628200	Active TSS	Right Ventricle	heart
6	chrX:153625200-153628600	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chrX:153625200-153628600	Active TSS	Psoas Muscle	Psoas
8	chrX:153625200-153628800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chrX:153625400-153627600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chrX:153625400-153627600	Active TSS	Primary T helper naive cells from peripheral blood	blood
11	chrX:153625400-153627600	Active TSS	Esophagus	oesophagus
12	chrX:153625400-153627600	Active TSS	Gastric	stomach
13	chrX:153625400-153627600	Active TSS	Sigmoid Colon	Sigmoid Colon
14	chrX:153625400-153627600	Active TSS	GM12878-XiMat	blood
15	chrX:153625400-153627600	Active TSS	HMEC	breast
16	chrX:153625400-153627800	Active TSS	Brain Cingulate Gyrus	brain
17	chrX:153625400-153627800	Active TSS	Brain Substantia Nigra	brain
18	chrX:153625400-153627800	Active TSS	Colon Smooth Muscle	Colon
19	chrX:153625400-153627800	Active TSS	Rectal Smooth Muscle	rectum
20	chrX:153625400-153627800	Active TSS	Small Intestine	intestine
21	chrX:153625400-153628000	Active TSS	Fetal Heart	heart
22	chrX:153625400-153628000	Active TSS	Placenta Amnion	Placenta Amnion
23	chrX:153625400-153628400	Active TSS	Ovary	ovary
24	chrX:153625400-153628800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chrX:153625400-153630000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
26	chrX:153625400-153631600	ZNF genes & repeats	Fetal Brain Female	brain
27	chrX:153625600-153627600	Active TSS	Aorta	Aorta
28	chrX:153625600-153627600	Active TSS	Spleen	Spleen
29	chrX:153625600-153627800	Active TSS	Stomach Mucosa	stomach
30	chrX:153625600-153627800	Active TSS	Thymus	Thymus
31	chrX:153625600-153628400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chrX:153625600-153629800	ZNF genes & repeats	Lung	lung
33	chrX:153625800-153627600	Bivalent/Poised TSS	Breast Myoepithelial Primary Cells	Breast
34	chrX:153625800-153627600	Active TSS	Primary T cells from cord blood	blood
35	chrX:153625800-153627600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chrX:153625800-153627800	Active TSS	Brain Germinal Matrix	brain
37	chrX:153626000-153627600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chrX:153626000-153627600	Active TSS	Colonic Mucosa	Colon
39	chrX:153626200-153628800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
40	chrX:153626400-153627600	ZNF genes & repeats	Fetal Brain Male	brain
41	chrX:153626400-153628200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
42	chrX:153626400-153628200	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
43	chrX:153626800-153628000	Flanking Active TSS	Primary hematopoietic stem cells	blood
44	chrX:153626800-153628600	Transcr. at gene 5' and 3'	NHEK	skin
45	chrX:153626800-153628800	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
46	chrX:153626800-153628800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
47	chrX:153626800-153628800	Transcr. at gene 5' and 3'	Dnd41	blood
48	chrX:153626800-153629000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chrX:153626800-153629600	Transcr. at gene 5' and 3'	A549	lung
50	chrX:153627000-153627600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood

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