Variant report

Variant	rs7625068
Chromosome Location	chr3:196255796-196255797
allele	C/T
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	CTCF	chr3:196255668-196255922	GM10248	blood:	n/a	chr3:196255804-196255814 chr3:196255801-196255822 chr3:196255799-196255817 chr3:196255802-196255811 chr3:196255802-196255815 chr3:196255800-196255816
2	POLR2A	chr3:196255361-196256067	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:196255525-196256131	HUVEC	blood vessel:	n/a	n/a
4	ESR1	chr3:196255435-196255982	ECC-1	luminal epithelium:	n/a	n/a
5	ARID3A	chr3:196255645-196256010	K562	blood:	n/a	n/a
6	CTCF	chr3:196255760-196255910	GM12871	blood:	n/a	chr3:196255804-196255814 chr3:196255801-196255822 chr3:196255799-196255817 chr3:196255802-196255811 chr3:196255802-196255815 chr3:196255800-196255816
7	MYC	chr3:196255714-196256281	H1-hESC	embryonic stem cell:	n/a	chr3:196255768-196255778
8	E2F6	chr3:196255353-196256141	A549	lung:	n/a	n/a
9	E2F6	chr3:196255383-196255913	K562	blood:	n/a	n/a
10	CTCF	chr3:196255720-196255870	HRPEpiC	eye:	n/a	chr3:196255804-196255814 chr3:196255801-196255822 chr3:196255799-196255817 chr3:196255802-196255811 chr3:196255802-196255815 chr3:196255800-196255816
11	POLR2A	chr3:196255678-196256022	SK-N-SH	brain:	n/a	n/a
12	YY1	chr3:196255642-196256061	SK-N-SH_RA	brain:	n/a	chr3:196255696-196255710 chr3:196255805-196255819 chr3:196255701-196255710 chr3:196255808-196255822
13	TCF7L2	chr3:196255488-196256014	HCT-116	colon:	n/a	chr3:196255926-196255942
14	TAF1	chr3:196255519-196256043	GM12892	blood:	n/a	n/a
15	POLR2A	chr3:196255441-196256098	GM15510	blood:	n/a	n/a
16	NANOG	chr3:196255584-196256017	H1-hESC	embryonic stem cell:	n/a	n/a
17	CTCF	chr3:196255476-196256025	H1-hESC	embryonic stem cell:	n/a	chr3:196255804-196255814 chr3:196255801-196255822 chr3:196255799-196255817 chr3:196255802-196255811 chr3:196255802-196255815 chr3:196255800-196255816
18	BCLAF1	chr3:196255328-196256090	GM12878	blood:	n/a	chr3:196255700-196255709 chr3:196255697-196255710 chr3:196255770-196255783
19	CTCF	chr3:196255606-196255943	A549	lung:	n/a	chr3:196255804-196255814 chr3:196255801-196255822 chr3:196255799-196255817 chr3:196255802-196255811 chr3:196255802-196255815 chr3:196255800-196255816
20	CTCF	chr3:196255780-196255930	GM12872	blood:	n/a	chr3:196255804-196255814 chr3:196255801-196255822 chr3:196255799-196255817 chr3:196255802-196255811 chr3:196255802-196255815 chr3:196255800-196255816
21	CTCF	chr3:196255700-196255850	GM12866	blood:	n/a	chr3:196255804-196255814 chr3:196255801-196255822 chr3:196255799-196255817 chr3:196255802-196255811 chr3:196255802-196255815 chr3:196255800-196255816
22	TFAP2A	chr3:196255522-196256170	Hela-S3	cervix:	n/a	n/a
23	ELK1	chr3:196255631-196255908	GM12878	blood:	n/a	n/a
24	CTCF	chr3:196255760-196255910	AG09309	skin:	n/a	chr3:196255804-196255814 chr3:196255801-196255822 chr3:196255799-196255817 chr3:196255802-196255811 chr3:196255802-196255815 chr3:196255800-196255816
25	RCOR1	chr3:196255582-196255980	K562	blood:	n/a	n/a
26	POLR2A	chr3:196255355-196256062	A549	lung:	n/a	n/a
27	CTCF	chr3:196255760-196255910	Caco-2	colon:	n/a	chr3:196255804-196255814 chr3:196255801-196255822 chr3:196255799-196255817 chr3:196255802-196255811 chr3:196255802-196255815 chr3:196255800-196255816
28	UBTF	chr3:196255492-196255991	K562	blood:	n/a	n/a
29	TAF1	chr3:196255659-196256069	SK-N-SH	brain:	n/a	n/a
30	POLR2A	chr3:196255551-196255928	GM12878	blood:	n/a	n/a
31	CTCF	chr3:196255780-196255930	HPAF	blood vessel:	n/a	chr3:196255804-196255814 chr3:196255801-196255822 chr3:196255799-196255817 chr3:196255802-196255811 chr3:196255802-196255815 chr3:196255800-196255816
32	POLR2A	chr3:196255354-196256115	GM12892	blood:	n/a	n/a
33	TBP	chr3:196255581-196256089	K562	blood:	n/a	n/a
34	PAX5	chr3:196255372-196255896	GM12878	blood:	n/a	n/a
35	POLR2A	chr3:196255442-196256096	MCF10A-Er-Src	breast:	n/a	n/a
36	STAT5A	chr3:196255310-196256069	GM12878	blood:	n/a	n/a
37	GABPA	chr3:196255486-196255837	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr3:196255387-196256149	HUVEC	blood vessel:	n/a	n/a
39	REST	chr3:196255747-196255911	GM12878	blood:	n/a	chr3:196255753-196255763
40	CTCF	chr3:196255760-196255910	GM12872	blood:	n/a	chr3:196255804-196255814 chr3:196255801-196255822 chr3:196255799-196255817 chr3:196255802-196255811 chr3:196255802-196255815 chr3:196255800-196255816
41	POLR2A	chr3:196255521-196256119	HCT-116	colon:	n/a	n/a
42	CTCF	chr3:196255645-196255914	GM13976	blood:	n/a	chr3:196255804-196255814 chr3:196255801-196255822 chr3:196255799-196255817 chr3:196255802-196255811 chr3:196255802-196255815 chr3:196255800-196255816
43	MAX	chr3:196255355-196256294	H1-hESC	embryonic stem cell:	n/a	chr3:196255768-196255778
44	ETS1	chr3:196255438-196256003	K562	blood:	n/a	chr3:196255771-196255782
45	CTCF	chr3:196255780-196255930	BE2_C	brain:	n/a	chr3:196255804-196255814 chr3:196255801-196255822 chr3:196255799-196255817 chr3:196255802-196255811 chr3:196255802-196255815 chr3:196255800-196255816
46	CTCF	chr3:196255740-196255890	K562	blood:	n/a	chr3:196255804-196255814 chr3:196255801-196255822 chr3:196255799-196255817 chr3:196255802-196255811 chr3:196255802-196255815 chr3:196255800-196255816
47	CTCF	chr3:196255702-196255903	HepG2	liver:	n/a	chr3:196255804-196255814 chr3:196255801-196255822 chr3:196255799-196255817 chr3:196255802-196255811 chr3:196255802-196255815 chr3:196255800-196255816
48	CTCF	chr3:196255740-196255890	HMEC	breast:	n/a	chr3:196255804-196255814 chr3:196255801-196255822 chr3:196255799-196255817 chr3:196255802-196255811 chr3:196255802-196255815 chr3:196255800-196255816
49	YY1	chr3:196255369-196256229	H1-hESC	embryonic stem cell:	n/a	chr3:196255696-196255710 chr3:196255805-196255819 chr3:196255701-196255710 chr3:196255808-196255822
50	HEY1	chr3:196255411-196256074	K562	blood:	n/a	chr3:196255760-196255775

No.	Distal block	Cell Line	Cell type
1	chr2:55276186..55276706-chr3:196255375..196256006,2	HCT-116	colon:
2	chr3:196253926..196256027-chr3:196295277..196297106,2	K562	blood:
3	chr3:196255773..196256767-chr3:196411387..196411995,2	K562	blood:

Variant related genes	Relation type
ENSG00000213358	TF binding region
ENSG00000185798	Chromatin interaction
ENSG00000174013	Chromatin interaction
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs2054747	1.00[ASN][1000 genomes]
rs2341333	0.89[EUR][1000 genomes]
rs6583312	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6583314	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6583315	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6583316	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6767712	1.00[ASN][1000 genomes]
rs6768682	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6783108	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6786154	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6807731	1.00[ASN][1000 genomes]
rs7374776	1.00[ASN][1000 genomes]
rs7615630	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7616415	1.00[ASN][1000 genomes]
rs7623203	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7633212	1.00[ASN][1000 genomes]
rs7640505	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9866935	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003194	chr3:195960270-196342423	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv536894	chr3:195960270-196342423	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv1003066	chr3:196098763-196414159	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	esv2752687	chr3:196147690-196286690	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv948681	chr3:196148055-197007546	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
6	nsv1010483	chr3:196210054-196319543	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv536896	chr3:196210054-196319543	Strong transcription Weak transcription Enhancers Flanking Active TSS 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 target site	29 gene(s)	inside rSNPs	diseases
8	nsv1014692	chr3:196242249-196531824	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
9	esv2763750	chr3:196242261-196278366	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv878187	chr3:196245603-196554790	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
11	nsv967108	chr3:196255474-196263970	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196254600-196255800	Enhancers	HepG2	liver
2	chr3:196255000-196256000	Active TSS	K562	blood
3	chr3:196255000-196256200	Active TSS	A549	lung
4	chr3:196255200-196256200	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr3:196255200-196256200	Enhancers	Primary B cells from cord blood	blood
6	chr3:196255400-196255800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr3:196255400-196255800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:196255400-196255800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
9	chr3:196255400-196255800	Flanking Active TSS	Brain Cingulate Gyrus	brain
10	chr3:196255400-196255800	Active TSS	Brain Hippocampus Middle	brain
11	chr3:196255400-196255800	Bivalent/Poised TSS	Fetal Brain Female	brain
12	chr3:196255400-196255800	Active TSS	Fetal Lung	lung
13	chr3:196255400-196255800	Flanking Active TSS	Placenta	Placenta
14	chr3:196255400-196255800	Flanking Active TSS	Fetal Thymus	thymus
15	chr3:196255400-196255800	Active TSS	Gastric	stomach
16	chr3:196255400-196255800	Active TSS	Ovary	ovary
17	chr3:196255400-196255800	Flanking Active TSS	HMEC	breast
18	chr3:196255400-196256000	Active TSS	H9 Cell Line	embryonic stem cell
19	chr3:196255400-196256000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:196255400-196256000	Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr3:196255400-196256000	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr3:196255400-196256000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
23	chr3:196255400-196256000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr3:196255400-196256000	Active TSS	Primary monocytes fromperipheralblood	blood
25	chr3:196255400-196256000	Active TSS	Primary T helper naive cells from peripheral blood	blood
26	chr3:196255400-196256000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
27	chr3:196255400-196256000	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
28	chr3:196255400-196256000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr3:196255400-196256000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
30	chr3:196255400-196256000	Enhancers	Liver	Liver
31	chr3:196255400-196256000	Active TSS	Brain Anterior Caudate	brain
32	chr3:196255400-196256000	Active TSS	Colonic Mucosa	Colon
33	chr3:196255400-196256000	Active TSS	Colon Smooth Muscle	Colon
34	chr3:196255400-196256000	Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr3:196255400-196256000	Flanking Active TSS	Esophagus	oesophagus
36	chr3:196255400-196256000	Enhancers	Fetal Brain Male	brain
37	chr3:196255400-196256000	Enhancers	Fetal Heart	heart
38	chr3:196255400-196256000	Active TSS	Fetal Intestine Small	intestine
39	chr3:196255400-196256000	Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr3:196255400-196256000	Active TSS	Left Ventricle	heart
41	chr3:196255400-196256000	Flanking Active TSS	Lung	lung
42	chr3:196255400-196256000	Flanking Active TSS	Placenta Amnion	Placenta Amnion
43	chr3:196255400-196256000	Active TSS	Rectal Mucosa Donor 29	rectum
44	chr3:196255400-196256000	ZNF genes & repeats	Right Atrium	heart
45	chr3:196255400-196256000	Flanking Active TSS	Right Ventricle	heart
46	chr3:196255400-196256000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr3:196255400-196256000	Active TSS	Small Intestine	intestine
48	chr3:196255400-196256000	Active TSS	HSMMtube	muscle
49	chr3:196255400-196256000	Active TSS	HUVEC	blood vessel
50	chr3:196255400-196256000	Active TSS	Monocytes-CD14+_RO01746	blood

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