Variant report

Variant	rs2070816
Chromosome Location	chrX:153595418-153595419
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:50)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:50 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HEY1	chrX:153595164-153595446	K562	blood:	n/a	n/a
2	POLR2A	chrX:153592099-153599779	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chrX:153594612-153595609	HL-60	blood:	n/a	n/a
4	POLR2A	chrX:153592005-153599772	GM12878	blood:	n/a	n/a
5	POLR2A	chrX:153594200-153595426	A549	lung:	n/a	n/a
6	POLR2A	chrX:153594031-153595537	HepG2	liver:	n/a	n/a
7	PML	chrX:153594600-153595575	K562	blood:	n/a	n/a
8	POLR2A	chrX:153595162-153595765	GM12878	blood:	n/a	n/a
9	POLR2A	chrX:153594063-153595864	SK-N-MC	brain:	n/a	n/a
10	POLR2A	chrX:153592032-153601467	GM12892	blood:	n/a	n/a
11	POLR2A	chrX:153594859-153596070	HepG2	liver:	n/a	n/a
12	POLR2A	chrX:153594377-153595454	K562	blood:	n/a	n/a
13	POLR2A	chrX:153594141-153596114	GM12892	blood:	n/a	n/a
14	POLR2A	chrX:153591801-153598985	U87	brain:	n/a	n/a
15	POLR2A	chrX:153592083-153600058	K562	blood:	n/a	n/a
16	POLR2A	chrX:153595334-153595583	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chrX:153594277-153595556	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chrX:153594099-153595435	GM12878	blood:	n/a	n/a
19	POLR2A	chrX:153592084-153596144	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chrX:153594354-153595959	PANC-1	pancreas:	n/a	n/a
21	POLR2A	chrX:153591991-153595865	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chrX:153594723-153595741	K562	blood:	n/a	n/a
23	POLR2A	chrX:153594312-153595767	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chrX:153594379-153595428	MCF-7	breast:	n/a	n/a
25	TEAD4	chrX:153595093-153595786	K562	blood:	n/a	chrX:153595314-153595323
26	POLR2A	chrX:153594104-153595676	GM12892	blood:	n/a	n/a
27	POLR2A	chrX:153593135-153595802	K562	blood:	n/a	n/a
28	POLR2A	chrX:153595170-153595695	HUVEC	blood vessel:	n/a	n/a
29	POLR2A	chrX:153595159-153595457	HUVEC	blood vessel:	n/a	n/a
30	POLR2A	chrX:153592028-153600292	K562	blood:	n/a	n/a
31	POLR2A	chrX:153594895-153595427	SK-N-SH	brain:	n/a	n/a
32	POLR2A	chrX:153592104-153599761	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chrX:153591858-153600815	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chrX:153592114-153595625	HL-60	blood:	n/a	n/a
35	POLR2A	chrX:153594449-153595855	K562	blood:	n/a	n/a
36	POLR2A	chrX:153595191-153595525	ECC-1	luminal epithelium:	n/a	n/a
37	POLR2A	chrX:153592099-153598720	A549	lung:	n/a	n/a
38	POLR2A	chrX:153594270-153601377	ProgFib	skin:	n/a	n/a
39	POLR2A	chrX:153594289-153595427	GM12878	blood:	n/a	n/a
40	POLR2A	chrX:153591864-153600710	U87	brain:	n/a	n/a
41	POLR2A	chrX:153594231-153596077	HepG2	liver:	n/a	n/a
42	POLR2A	chrX:153592085-153600048	K562	blood:	n/a	n/a
43	POLR2A	chrX:153595054-153595451	GM12878	blood:	n/a	n/a
44	USF2	chrX:153594904-153595466	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chrX:153595193-153596441	U87	brain:	n/a	n/a
46	POLR2A	chrX:153591956-153600830	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chrX:153594275-153595434	GM12878	blood:	n/a	n/a
48	POLR2A	chrX:153595278-153596441	U87	brain:	n/a	n/a
49	HEY1	chrX:153594994-153595526	K562	blood:	n/a	n/a
50	POLR2A	chrX:153594213-153595463	Hela-S3	cervix:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chrX:153361067..153363781-chrX:153595090..153596698,2	K562	blood:
2	chrX:153595148..153597150-chrX:153772995..153774995,2	K562	blood:
3	chrX:153594250..153603496-chrX:153624447..153635089,39	K562	blood:
4	X:153586280-153597086..X:153719993-153730954	Hela-S3	cervix:
5	X:153586280-153597086..X:154053104-154056925	K562	blood:
6	chrX:153592401..153602834-chrX:153624077..153632705,30	K562	blood:
7	chrX:153595264..153612826-chrX:153621461..153634267,75	MCF-7	breast:
8	X:153586280-153597086..X:153614328-153625659	Hela-S3	cervix:
9	chrX:153594832..153597278-chrX:153711164..153713402,2	MCF-7	breast:
10	chrX:153594620..153614384-chrX:153624179..153643019,157	MCF-7	breast:
11	X:153586280-153597086..X:153657611-153671976	H1-hESC	embryonic stem cell:	embryo
12	chrX:153595338..153600468-chrX:153664217..153668349,5	K562	blood:

No data

Variant related genes	Relation type
FLNA	TF binding region
ENSG00000147403	Chromatin interaction
ENSG00000264783	Chromatin interaction
ENSG00000073009	Chromatin interaction
ENSG00000207165	Chromatin interaction
ENSG00000203879	Chromatin interaction
ENSG00000203870	Chromatin interaction
ENSG00000264631	Chromatin interaction
ENSG00000169057	Chromatin interaction
ENSG00000013563	Chromatin interaction
ENSG00000102125	Chromatin interaction
ENSG00000264484	Chromatin interaction
ENSG00000160211	Chromatin interaction
ENSG00000071553	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11593	0.90[ASW][hapmap];0.81[MKK][hapmap]
rs12007167	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap]
rs17426	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17428	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap]
rs2070807	0.80[ASW][hapmap]
rs2070822	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs2239470	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs28602900	0.80[ASW][hapmap]
rs2872817	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap]
rs4446899	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][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];0.92[JPT][hapmap]
rs5945423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs915943	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531228	chrX:152864376-153609161	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	nsv529439	chrX:153333946-153595528	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
6	nsv932632	chrX:153333946-153623000	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
7	nsv531232	chrX:153333946-153626120	Genic enhancers Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
8	nsv531233	chrX:153333946-153626120	Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
9	nsv523072	chrX:153333946-153626738	Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	146 gene(s)	inside rSNPs	diseases
10	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
11	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
12	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
13	nsv9999	chrX:153567427-153621413	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
14	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
15	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2070816	LAGE3	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:153576000-153596000	Weak transcription	Primary hematopoietic stem cells	blood
2	chrX:153576200-153595800	Weak transcription	Right Atrium	heart
3	chrX:153576200-153596600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chrX:153576400-153599400	ZNF genes & repeats	Fetal Stomach	stomach
5	chrX:153576600-153595800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chrX:153576600-153596400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chrX:153576600-153596400	Strong transcription	Thymus	Thymus
8	chrX:153576600-153596600	Strong transcription	H1 Cell Line	embryonic stem cell
9	chrX:153576600-153596600	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chrX:153576600-153596800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chrX:153576600-153598800	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
12	chrX:153576600-153599800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
13	chrX:153576800-153596000	Strong transcription	Brain Germinal Matrix	brain
14	chrX:153576800-153596000	Strong transcription	Placenta Amnion	Placenta Amnion
15	chrX:153576800-153603600	ZNF genes & repeats	Fetal Brain Female	brain
16	chrX:153577000-153595600	Strong transcription	Aorta	Aorta
17	chrX:153577200-153595600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chrX:153577400-153596000	Strong transcription	Ovary	ovary
19	chrX:153578000-153596800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chrX:153579400-153596800	Strong transcription	Fetal Intestine Small	intestine
21	chrX:153580200-153595800	Strong transcription	Sigmoid Colon	Sigmoid Colon
22	chrX:153580200-153596400	Genic enhancers	Primary T cells fromperipheralblood	blood
23	chrX:153580200-153598200	Weak transcription	Stomach Mucosa	stomach
24	chrX:153581000-153596000	Strong transcription	Colonic Mucosa	Colon
25	chrX:153581200-153595800	Weak transcription	Primary B cells from cord blood	blood
26	chrX:153581200-153596400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chrX:153581600-153596600	Weak transcription	Fetal Brain Male	brain
28	chrX:153582800-153596000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chrX:153584000-153596600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
30	chrX:153584800-153596600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chrX:153586000-153596600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chrX:153587400-153597000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chrX:153587400-153597200	Weak transcription	Psoas Muscle	Psoas
34	chrX:153587600-153596200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chrX:153587600-153596800	Weak transcription	Small Intestine	intestine
36	chrX:153589800-153596400	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chrX:153590000-153596000	Strong transcription	K562	blood
38	chrX:153590600-153596200	Strong transcription	Spleen	Spleen
39	chrX:153591400-153595800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chrX:153591400-153596600	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chrX:153592200-153597400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
42	chrX:153592200-153599400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
43	chrX:153592400-153595600	Strong transcription	Pancreas	Pancrea
44	chrX:153592600-153595600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
45	chrX:153592600-153596600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chrX:153592600-153596600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
47	chrX:153592800-153596400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chrX:153592800-153597000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
49	chrX:153593000-153596400	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chrX:153593400-153597000	Genic enhancers	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links