Variant report

Variant	rs11202875
Chromosome Location	chr10:90639774-90639775
allele	A/C
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	E2F4	chr10:90639687-90639887	MCF10A-Er-Src	breast:	n/a	n/a
2	TAF1	chr10:90639558-90641029	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr10:90639586-90641828	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr10:90639480-90641613	U87	brain:	n/a	n/a
5	POLR2A	chr10:90639409-90641040	GM12892	blood:	n/a	n/a
6	MAX	chr10:90639494-90640977	A549	lung:	n/a	chr10:90640816-90640826
7	POLR2A	chr10:90639614-90640945	GM12878	blood:	n/a	n/a
8	POLR2A	chr10:90639531-90641494	GM18951	blood:	n/a	n/a
9	BHLHE40	chr10:90639378-90640927	GM12878	blood:	n/a	chr10:90640674-90640690
10	MXI1	chr10:90639555-90641039	GM12878	blood:	n/a	n/a
11	RELA	chr10:90639656-90640919	GM19193	blood:	n/a	n/a
12	POLR2A	chr10:90639757-90640952	MCF-7	breast:	n/a	n/a
13	STAT1	chr10:90639768-90640950	GM12878	blood:	n/a	chr10:90640658-90640666
14	WRNIP1	chr10:90639531-90640975	GM12878	blood:	n/a	n/a
15	TAF1	chr10:90639624-90640943	GM12878	blood:	n/a	n/a
16	RAD21	chr10:90639665-90640999	ECC-1	luminal epithelium:	n/a	chr10:90640670-90640684
17	POLR2A	chr10:90639563-90641024	GM12891	blood:	n/a	n/a
18	YY1	chr10:90639765-90640791	GM12891	blood:	n/a	chr10:90639922-90639931 chr10:90639917-90639931 chr10:90639919-90639928 chr10:90640598-90640607 chr10:90639919-90639930
19	TCF3	chr10:90639660-90640760	GM12878	blood:	n/a	n/a
20	TCF12	chr10:90639595-90641139	A549	lung:	n/a	n/a
21	TAF1	chr10:90639721-90640483	GM12891	blood:	n/a	n/a
22	MTA3	chr10:90639449-90640307	GM12878	blood:	n/a	n/a
23	MAX	chr10:90639660-90640949	MCF-7	breast:	n/a	chr10:90640816-90640826
24	POLR2A	chr10:90639293-90641628	GM12892	blood:	n/a	n/a
25	ZKSCAN1	chr10:90639600-90640908	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr10:90639521-90641000	HL-60	blood:	n/a	n/a
27	TEAD4	chr10:90639599-90640824	ECC-1	luminal epithelium:	n/a	n/a
28	KAP1	chr10:90639269-90640641	HEK293	kidney:	n/a	n/a
29	ZEB1	chr10:90639774-90640951	GM12878	blood:	n/a	chr10:90640925-90640937 chr10:90640927-90640934
30	TAF1	chr10:90639622-90639893	GM12892	blood:	n/a	n/a
31	HA-E2F1	chr10:90639758-90640843	Hela-S3	cervix:	n/a	chr10:90639917-90639927 chr10:90639920-90639930 chr10:90640546-90640553
32	POLR2A	chr10:90639591-90641016	GM12891	blood:	n/a	n/a
33	YY1	chr10:90639582-90640925	ECC-1	luminal epithelium:	n/a	chr10:90639922-90639931 chr10:90639917-90639931 chr10:90639919-90639928 chr10:90640598-90640607 chr10:90639919-90639930
34	BCLAF1	chr10:90639559-90641144	GM12878	blood:	n/a	chr10:90639918-90639927 chr10:90639921-90639930 chr10:90639918-90639931
35	REST	chr10:90639720-90640575	SK-N-SH	brain:	n/a	n/a
36	TAF1	chr10:90639721-90640041	SK-N-SH	brain:	n/a	n/a
37	POLR2A	chr10:90639363-90641045	HL-60	blood:	n/a	n/a
38	POLR2A	chr10:90639648-90640949	GM12878	blood:	n/a	n/a
39	RFX5	chr10:90639434-90640877	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr10:90639722-90640870	HCT-116	colon:	n/a	n/a
41	MYC	chr10:90639496-90639828	MCF10A-Er-Src	breast:	n/a	n/a
42	POLR2A	chr10:90639733-90640809	HCT-116	colon:	n/a	n/a
43	POLR2A	chr10:90639519-90641333	GM15510	blood:	n/a	n/a
44	POLR2A	chr10:90639558-90641614	U87	brain:	n/a	n/a
45	RELA	chr10:90639550-90641028	GM19099	blood:	n/a	n/a
46	TAF1	chr10:90639625-90640880	SK-N-SH	brain:	n/a	n/a
47	POLR2A	chr10:90639689-90641264	MCF10A-Er-Src	breast:	n/a	n/a
48	MYC	chr10:90639569-90641297	Hela-S3	cervix:	n/a	chr10:90640816-90640826
49	RELA	chr10:90639533-90640941	GM10847	blood:	n/a	n/a
50	EP300	chr10:90639535-90641084	SK-N-SH	brain:	n/a	chr10:90639920-90639929 chr10:90640598-90640607 chr10:90639917-90639926

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr10:90639746-90639796	IMR90	lung:	fetal
2	chr10:90639746-90639796	HAEpiC	amniotic membrane:	n/a
3	chr10:90639746-90639796	GM12878	blood:	n/a
4	chr10:90639746-90639796	PFSK-1	brain:	n/a
5	chr10:90639746-90639796	HEK293	kidney:	embryo
6	chr10:90639746-90639796	GM12892	blood:	n/a
7	chr10:90639746-90639796	HCPEpiC	choroid plexus:	n/a
8	chr10:90639746-90639796	AG09309	skin:	n/a
9	chr10:90639746-90639796	AG10803	skin:	n/a
10	chr10:90639746-90639796	HEEpiC	esophagus:	n/a
11	chr10:90639746-90639796	Hela-S3	cervix:	n/a
12	chr10:90639746-90639796	GM19239	blood:	n/a
13	chr10:90639746-90639796	PrEC	prostate:	n/a
14	chr10:90639746-90639796	AG04449	skin:	fetal
15	chr10:90639746-90639796	U87	brain:	n/a
16	chr10:90639746-90639796	SK-N-SH	brain:	n/a
17	chr10:90639746-90639796	HNPCEpiC	eye:	n/a
18	chr10:90639746-90639796	HPAEpiC	pulmonary alveolar:	n/a
19	chr10:90639746-90639796	HepG2	liver:	n/a
20	chr10:90639746-90639796	SK-N-MC	brain:	n/a
21	chr10:90639746-90639796	CMK	blood:	n/a
22	chr10:90639746-90639796	HL-60	blood:	n/a
23	chr10:90639746-90639796	NB4	blood:	n/a
24	chr10:90639746-90639796	ECC-1	luminal epithelium:	n/a
25	chr10:90639746-90639796	Caco-2	colon:	n/a
26	chr10:90639746-90639796	BE2_C	brain:	n/a
27	chr10:90639746-90639796	BJ	skin:	n/a
28	chr10:90639746-90639796	HUVEC	blood vessel:	n/a
29	chr10:90639746-90639796	HMEC	breast:	n/a
30	chr10:90639746-90639796	RPTEC	kidney:	n/a
31	chr10:90639746-90639796	GM06990	blood:	n/a
32	chr10:90639746-90639796	HRCEpiC	kidney:	n/a
33	chr10:90639746-90639796	H1-hESC	embryonic stem cell:	embryo
34	chr10:90639746-90639796	SKMC	muscle:	n/a
35	chr10:90639746-90639796	PANC-1	pancreas:	n/a
36	chr10:90639746-90639796	NT2-D1	testis:	n/a
37	chr10:90639746-90639796	MCF-7	breast:	n/a
38	chr10:90639746-90639796	Hepatocyte	liver:	n/a
39	chr10:90639746-90639796	ovcar-3	ovarian:	n/a
40	chr10:90639746-90639796	HCF	heart:	n/a
41	chr10:90639746-90639796	Jurkat	blood:	n/a
42	chr10:90639746-90639796	HCM	heart:	n/a
43	chr10:90639746-90639796	MCF10A-Er-Src	breast:	n/a
44	chr10:90639746-90639796	HRPEpiC	eye:	n/a
45	chr10:90639746-90639796	T-47D	breast:	n/a
46	chr10:90639746-90639796	AG09319	gingival:	n/a
47	chr10:90639746-90639796	NHBE	bronchial:	n/a
48	chr10:90639746-90639796	LNCaP	prostate:	n/a
49	chr10:90639746-90639796	NHDF-neo	bronchial:	n/a
50	chr10:90639746-90639796	ProgFib	skin:	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:90639266..90639790-chr6:89790419..89791128,2	Hela-S3	cervix:
2	chr10:90639734..90640291-chr9:86595257..86596036,2	Hela-S3	cervix:
3	chr10:90639301..90642051-chr10:90749823..90751899,2	MCF-7	breast:
4	chr1:46151781..46152462-chr10:90639721..90640246,2	Hela-S3	cervix:
5	chr10:90634887..90637855-chr10:90638729..90640945,2	MCF-7	breast:
6	chr1:150550552..150551301-chr10:90639551..90640288,2	Hela-S3	cervix:

Variant related genes	Relation type
STAMBPL1	TF binding region
STAMBPL1	CpG island
ENSG00000026103	Chromatin interaction
ENSG00000178966	Chromatin interaction
ENSG00000143384	Chromatin interaction
ENSG00000165119	Chromatin interaction
ENSG00000234256	Chromatin interaction
ENSG00000146278	Chromatin interaction
ENSG00000159592	Chromatin interaction
ENSG00000107796	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12242191	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs12247227	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12261664	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12264840	1.00[CEU][hapmap]
rs17096285	1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.91[EUR][1000 genomes]
rs17113560	0.93[GIH][hapmap]
rs17114120	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs17114161	0.85[GIH][hapmap];0.87[AMR][1000 genomes]
rs17114186	1.00[CEU][hapmap];0.93[GIH][hapmap];0.87[AMR][1000 genomes]
rs2147416	1.00[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.91[EUR][1000 genomes]
rs3758487	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs3781212	0.87[AMR][1000 genomes]
rs41284112	0.91[EUR][1000 genomes]
rs45473701	0.91[EUR][1000 genomes]
rs59597720	0.91[EUR][1000 genomes]
rs59889518	0.91[EUR][1000 genomes]
rs6586153	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7077534	1.00[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap]
rs7077849	0.91[EUR][1000 genomes]
rs7077956	1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.91[EUR][1000 genomes]
rs74147301	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74147448	0.83[EUR][1000 genomes]
rs74150103	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7899463	1.00[CEU][hapmap]
rs7904718	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7906786	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7908124	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7911566	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529324	chr10:90198865-90738588	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv831942	chr10:90564697-90730352	Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90638200-90639800	Flanking Active TSS	Dnd41	blood
2	chr10:90639000-90639800	Flanking Active TSS	Hela-S3	cervix
3	chr10:90639000-90639800	Flanking Active TSS	NHLF	lung
4	chr10:90639000-90642200	Active TSS	Rectal Smooth Muscle	rectum
5	chr10:90639200-90639800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
6	chr10:90639200-90639800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
7	chr10:90639200-90639800	Flanking Active TSS	Primary T cells from cord blood	blood
8	chr10:90639200-90639800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
9	chr10:90639200-90639800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
10	chr10:90639200-90639800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
11	chr10:90639200-90639800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
12	chr10:90639200-90639800	Flanking Active TSS	Adipose Nuclei	Adipose
13	chr10:90639200-90639800	Flanking Active TSS	Liver	Liver
14	chr10:90639200-90639800	Flanking Active TSS	Brain Anterior Caudate	brain
15	chr10:90639200-90639800	Flanking Active TSS	Duodenum Mucosa	Duodenum
16	chr10:90639200-90639800	Flanking Active TSS	Fetal Lung	lung
17	chr10:90639200-90639800	Flanking Active TSS	GM12878-XiMat	blood
18	chr10:90639200-90640000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr10:90639200-90640000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr10:90639200-90640000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
21	chr10:90639200-90640200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr10:90639200-90640800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr10:90639200-90641200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr10:90639200-90642000	Active TSS	Brain Cingulate Gyrus	brain
25	chr10:90639200-90642000	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr10:90639200-90642400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr10:90639400-90639800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
28	chr10:90639400-90639800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
29	chr10:90639400-90639800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
30	chr10:90639400-90639800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr10:90639400-90639800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
32	chr10:90639400-90639800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr10:90639400-90639800	Flanking Active TSS	Primary hematopoietic stem cells	blood
34	chr10:90639400-90639800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
35	chr10:90639400-90639800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
36	chr10:90639400-90639800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
37	chr10:90639400-90639800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr10:90639400-90639800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
39	chr10:90639400-90639800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
40	chr10:90639400-90639800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr10:90639400-90639800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
42	chr10:90639400-90639800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
43	chr10:90639400-90639800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr10:90639400-90639800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr10:90639400-90639800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr10:90639400-90639800	Flanking Active TSS	Fetal Brain Female	brain
47	chr10:90639400-90639800	Flanking Active TSS	Fetal Intestine Large	intestine
48	chr10:90639400-90639800	Flanking Active TSS	Fetal Intestine Small	intestine
49	chr10:90639400-90639800	Flanking Bivalent TSS/Enh	Fetal Kidney	kidney
50	chr10:90639400-90639800	Flanking Active TSS	Fetal Muscle Leg	muscle

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