Variant report

Variant	rs6585018
Chromosome Location	chr10:112631211-112631212
allele	A/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	SP1	chr10:112631200-112631813	GM12878	blood:	n/a	chr10:112631427-112631437 chr10:112631609-112631630 chr10:112631518-112631527
2	RAD21	chr10:112631118-112631813	SK-N-SH_RA	brain:	n/a	chr10:112631621-112631633
3	TAF1	chr10:112630984-112632518	ECC-1	luminal epithelium:	n/a	n/a
4	TBP	chr10:112630899-112632099	GM12878	blood:	n/a	n/a
5	USF2	chr10:112631155-112631722	Hela-S3	cervix:	n/a	chr10:112631472-112631488
6	SMC3	chr10:112630974-112632858	Hela-S3	cervix:	n/a	chr10:112632212-112632222
7	TEAD4	chr10:112631177-112631585	H1-hESC	embryonic stem cell:	n/a	n/a
8	TCF12	chr10:112631047-112632763	ECC-1	luminal epithelium:	n/a	n/a
9	YY1	chr10:112631135-112631449	A549	lung:	n/a	n/a
10	RFX5	chr10:112631062-112632976	Hela-S3	cervix:	n/a	n/a
11	TAF1	chr10:112631114-112632815	H1-neurons	neurons:	n/a	n/a
12	BCL3	chr10:112630908-112631519	A549	lung:	n/a	n/a
13	POLR2A	chr10:112631092-112632824	HepG2	liver:	n/a	n/a
14	MAX	chr10:112631178-112632925	GM12878	blood:	n/a	chr10:112632424-112632431 chr10:112632814-112632822 chr10:112632041-112632051 chr10:112632423-112632434 chr10:112632422-112632435 chr10:112632424-112632433 chr10:112632423-112632434 chr10:112632275-112632285
15	POLR2A	chr10:112631153-112632826	K562	blood:	n/a	n/a
16	ZNF263	chr10:112630575-112632800	HEK293-T-REx	kidney:	n/a	chr10:112632115-112632124
17	MAX	chr10:112631166-112632842	H1-hESC	embryonic stem cell:	n/a	chr10:112632424-112632431 chr10:112632814-112632822 chr10:112632041-112632051 chr10:112632423-112632434 chr10:112632422-112632435 chr10:112632424-112632433 chr10:112632423-112632434 chr10:112632275-112632285
18	POLR2A	chr10:112631121-112632744	GM12878	blood:	n/a	n/a
19	POLR2A	chr10:112630523-112633327	GM18505	blood:	n/a	n/a
20	POLR2A	chr10:112631095-112632760	H1-hESC	embryonic stem cell:	n/a	n/a
21	SP1	chr10:112631060-112632791	A549	lung:	n/a	chr10:112632378-112632390 chr10:112632293-112632307 chr10:112632040-112632049 chr10:112632038-112632050 chr10:112632653-112632665 chr10:112631427-112631437 chr10:112632210-112632219 chr10:112632380-112632389 chr10:112632209-112632223 chr10:112632655-112632664 chr10:112632653-112632665 chr10:112632654-112632668 chr10:112632209-112632218 chr10:112632208-112632220 chr10:112632209-112632218 chr10:112631609-112631630 chr10:112632038-112632050 chr10:112632208-112632220 chr10:112632378-112632390 chr10:112631518-112631527 chr10:112632039-112632048
22	EP300	chr10:112631173-112631820	T-47D	breast:	n/a	n/a
23	TBP	chr10:112630608-112633283	K562	blood:	n/a	n/a
24	POLR2A	chr10:112631099-112632707	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr10:112631050-112632380	U87	brain:	n/a	n/a
26	SIN3AK20	chr10:112630879-112633003	MCF-7	breast:	n/a	n/a
27	POLR2A	chr10:112630852-112633006	HL-60	blood:	n/a	n/a
28	EGR1	chr10:112631132-112632408	HCT-116	colon:	n/a	chr10:112632042-112632052 chr10:112632041-112632054 chr10:112631864-112631878 chr10:112631631-112631640 chr10:112632041-112632054 chr10:112631500-112631509 chr10:112632211-112632224
29	POLR2A	chr10:112630780-112632929	MCF-7	breast:	n/a	n/a
30	POLR2A	chr10:112631116-112632777	K562	blood:	n/a	n/a
31	POLR2A	chr10:112631148-112631985	HUVEC	blood vessel:	n/a	n/a
32	ZNF143	chr10:112631155-112632728	GM12878	blood:	n/a	chr10:112632407-112632417 chr10:112632145-112632163
33	POLR2A	chr10:112631152-112632457	Gliobla	brain:	n/a	n/a
34	POLR2A	chr10:112631135-112632899	GM12891	blood:	n/a	n/a
35	ZBTB7A	chr10:112631010-112632878	ECC-1	luminal epithelium:	n/a	chr10:112632329-112632340
36	MAX	chr10:112631105-112632911	HepG2	liver:	n/a	chr10:112632424-112632431 chr10:112632814-112632822 chr10:112632041-112632051 chr10:112632423-112632434 chr10:112632422-112632435 chr10:112632424-112632433 chr10:112632423-112632434 chr10:112632275-112632285
37	CHD1	chr10:112630906-112633586	GM12878	blood:	n/a	chr10:112632208-112632218 chr10:112632079-112632089
38	RUNX3	chr10:112630658-112631576	GM12878	blood:	n/a	n/a
39	POLR2A	chr10:112631134-112632753	GM12878	blood:	n/a	n/a
40	POLR2A	chr10:112630855-112632845	K562	blood:	n/a	n/a
41	POLR2A	chr10:112631191-112631539	H1-hESC	embryonic stem cell:	n/a	n/a
42	MYC	chr10:112631186-112631609	H1-hESC	embryonic stem cell:	n/a	n/a
43	RCOR1	chr10:112631067-112632916	Hela-S3	cervix:	n/a	n/a
44	MYC	chr10:112631151-112632863	K562	blood:	n/a	chr10:112632424-112632431 chr10:112632814-112632822 chr10:112632041-112632051 chr10:112632423-112632434 chr10:112632422-112632435 chr10:112632424-112632433 chr10:112632423-112632434 chr10:112632275-112632285
45	POLR2A	chr10:112631163-112632520	A549	lung:	n/a	n/a
46	POLR2A	chr10:112631127-112632448	MCF-7	breast:	n/a	n/a
47	NFYA	chr10:112631128-112631772	Hela-S3	cervix:	n/a	chr10:112631608-112631623 chr10:112631608-112631626 chr10:112631608-112631622 chr10:112631608-112631623
48	CREB1	chr10:112631112-112632901	GM12878	blood:	n/a	n/a
49	REST	chr10:112631057-112631653	A549	lung:	n/a	n/a
50	TCF12	chr10:112631193-112631537	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:112631001..112634625-chr10:112648231..112651298,3	MCF-7	breast:
2	chr10:112630838..112635784-chr10:112676837..112681433,10	K562	blood:
3	chr10:112327690..112330485-chr10:112631078..112633307,2	K562	blood:
4	chr10:112630522..112633740-chr10:112677502..112680452,8	K562	blood:
5	chr10:112594090..112596413-chr10:112629473..112632431,2	K562	blood:
6	chr10:112629865..112631826-chr10:112663124..112665657,2	K562	blood:
7	chr10:112630933..112635987-chr10:112638238..112642004,12	MCF-7	breast:
8	chr10:112581723..112584048-chr10:112629413..112632345,2	K562	blood:
9	chr10:112581444..112587243-chr10:112629842..112633404,6	MCF-7	breast:
10	chr10:112631125..112631745-chr7:150782860..150783599,2	NB4	blood:
11	chr10:112580755..112589346-chr10:112627817..112636075,27	MCF-7	breast:
12	chr10:112630166..112634091-chr10:112649118..112655902,7	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PDCD4-1	chr10:112631051-112631352	XLOC_008612
2	lnc-BBIP1-1	chr10:112628648-112631552	NONHSAT016362

Variant related genes	Relation type
PDCD4	TF binding region
ENSG00000203867	Chromatin interaction
ENSG00000150593	Chromatin interaction
ENSG00000108055	Chromatin interaction
ENSG00000108061	Chromatin interaction
ENSG00000214413	Chromatin interaction
ENSG00000133612	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10885075	0.85[GIH][hapmap]
rs11195368	1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs11195373	0.87[EUR][1000 genomes]
rs11195376	0.92[EUR][1000 genomes]
rs11195409	0.81[EUR][1000 genomes]
rs11592186	0.92[EUR][1000 genomes]
rs11592376	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs11593462	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11593479	0.92[EUR][1000 genomes]
rs11593592	1.00[MEX][hapmap];0.86[TSI][hapmap];0.92[EUR][1000 genomes]
rs11593866	0.82[EUR][1000 genomes]
rs11597120	0.92[EUR][1000 genomes]
rs11597460	0.92[EUR][1000 genomes]
rs11597928	1.00[EUR][1000 genomes]
rs11598889	1.00[CEU][hapmap]
rs11812232	0.81[EUR][1000 genomes]
rs11812855	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11813262	0.92[EUR][1000 genomes]
rs11813593	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11814418	1.00[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs11814686	0.92[EUR][1000 genomes]
rs11816033	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs11816247	0.81[GIH][hapmap];1.00[MEX][hapmap];0.92[EUR][1000 genomes]
rs11816269	1.00[MEX][hapmap];0.86[TSI][hapmap];0.92[EUR][1000 genomes]
rs11816396	0.92[EUR][1000 genomes]
rs11818060	0.92[EUR][1000 genomes]
rs11818747	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11818761	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11818771	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs11818869	1.00[CEU][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.92[EUR][1000 genomes]
rs1322997	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1327556	0.92[EUR][1000 genomes]
rs1535559	0.97[EUR][1000 genomes]
rs17128189	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1885796	1.00[CEU][hapmap];0.86[TSI][hapmap];0.92[EUR][1000 genomes]
rs34104444	0.92[EUR][1000 genomes]
rs4917589	0.90[GIH][hapmap]
rs55647014	0.97[EUR][1000 genomes]
rs55858908	0.97[EUR][1000 genomes]
rs56237211	0.97[EUR][1000 genomes]
rs60633872	0.92[EUR][1000 genomes]
rs60681723	0.94[EUR][1000 genomes]
rs60877808	0.86[EUR][1000 genomes]
rs61469604	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6585020	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7081726	1.00[GIH][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74156304	0.87[EUR][1000 genomes]
rs74156305	0.94[EUR][1000 genomes]
rs74156307	1.00[EUR][1000 genomes]
rs74156308	0.97[EUR][1000 genomes]
rs74156309	0.92[EUR][1000 genomes]
rs74156310	0.92[EUR][1000 genomes]
rs74156311	0.92[EUR][1000 genomes]
rs74156320	0.92[EUR][1000 genomes]
rs74156323	0.92[EUR][1000 genomes]
rs7923004	1.00[ASW][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045608	chr10:112524813-112677557	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1041758	chr10:112552897-112677557	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv896003	chr10:112579299-112631211	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv896002	chr10:112579299-112638028	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1051566	chr10:112580049-112730573	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:112630000-112631400	Flanking Active TSS	Primary T cells from cord blood	blood
2	chr10:112630200-112631400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
3	chr10:112630200-112631400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
4	chr10:112630400-112631400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr10:112630400-112631400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
6	chr10:112630400-112631400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
7	chr10:112630400-112631400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
8	chr10:112630400-112631400	Flanking Active TSS	Stomach Smooth Muscle	stomach
9	chr10:112630400-112631400	Flanking Active TSS	GM12878-XiMat	blood
10	chr10:112630400-112631800	Flanking Active TSS	Primary B cells from cord blood	blood
11	chr10:112630600-112631400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr10:112630600-112631400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr10:112630600-112631400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
14	chr10:112630600-112631400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
15	chr10:112630600-112631400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
16	chr10:112630600-112631400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr10:112630600-112631400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr10:112630600-112631400	Flanking Active TSS	Adipose Nuclei	Adipose
19	chr10:112630600-112631400	Flanking Active TSS	Rectal Smooth Muscle	rectum
20	chr10:112630600-112631400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
21	chr10:112630600-112631400	Flanking Active TSS	Dnd41	blood
22	chr10:112630600-112631400	Flanking Active TSS	K562	blood
23	chr10:112630600-112631600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
24	chr10:112630800-112631400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr10:112630800-112631400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr10:112630800-112631400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr10:112630800-112631400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr10:112630800-112631400	Flanking Active TSS	Primary B cells from peripheral blood	blood
29	chr10:112630800-112631400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
30	chr10:112630800-112631400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
31	chr10:112630800-112631400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr10:112630800-112631400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
33	chr10:112630800-112631400	Flanking Active TSS	Liver	Liver
34	chr10:112630800-112631400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
35	chr10:112630800-112631400	Flanking Active TSS	Fetal Brain Male	brain
36	chr10:112630800-112631400	Flanking Active TSS	Fetal Intestine Small	intestine
37	chr10:112630800-112631400	Flanking Active TSS	Fetal Lung	lung
38	chr10:112630800-112631400	Flanking Active TSS	Fetal Muscle Trunk	muscle
39	chr10:112630800-112631400	Flanking Active TSS	Fetal Muscle Leg	muscle
40	chr10:112630800-112631400	Flanking Active TSS	Fetal Thymus	thymus
41	chr10:112630800-112631400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
42	chr10:112630800-112631400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr10:112630800-112631400	Flanking Active TSS	Stomach Mucosa	stomach
44	chr10:112630800-112631400	Flanking Active TSS	A549	lung
45	chr10:112630800-112631400	Flanking Active TSS	Hela-S3	cervix
46	chr10:112630800-112631400	Flanking Active TSS	HUVEC	blood vessel
47	chr10:112630800-112631400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
48	chr10:112630800-112631400	Flanking Active TSS	NHDF-Ad	bronchial
49	chr10:112630800-112631600	Flanking Active TSS	Primary hematopoietic stem cells	blood
50	chr10:112630800-112631600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood

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