Variant report

Variant	rs7617236
Chromosome Location	chr3:196000443-196000444
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TBP	chr3:196000358-196000818	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr3:196000068-196000996	H1-hESC	embryonic stem cell:	n/a	n/a
3	SP1	chr3:196000306-196000928	H1-hESC	embryonic stem cell:	n/a	n/a
4	SP1	chr3:196000402-196000850	H1-hESC	embryonic stem cell:	n/a	n/a
5	ELF1	chr3:196000355-196000818	GM12878	blood:	n/a	chr3:196000594-196000607
6	SETDB1	chr3:195999858-196000535	K562	blood:	n/a	n/a
7	POLR2A	chr3:196000382-196000699	H1-hESC	embryonic stem cell:	n/a	n/a
8	SETDB1	chr3:196000077-196000583	U2OS	brain:	n/a	n/a
9	GABPA	chr3:196000251-196000643	H1-hESC	embryonic stem cell:	n/a	n/a
10	TAF1	chr3:196000255-196000877	H1-hESC	embryonic stem cell:	n/a	n/a
11	CBX3	chr3:196000079-196000597	K562	blood:	n/a	n/a
12	YY1	chr3:196000377-196000703	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr3:196000266-196000773	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr3:196000371-196000637	H1-hESC	embryonic stem cell:	n/a	n/a
15	CEBPB	chr3:196000203-196000555	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr3:196000356-196000683	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:195999654..196002310-chr3:196064662..196066658,2	K562	blood:
2	chr3:195971988..195973828-chr3:195999663..196002125,2	MCF-7	breast:
3	chr3:195999931..196002066-chr3:196007732..196009524,2	MCF-7	breast:

No data

Variant related genes	Relation type
PCYT1A	TF binding region
ENSG00000145107	Chromatin interaction
ENSG00000273331	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11185519	0.82[ASN][1000 genomes]
rs12632779	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12633454	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12633827	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12634350	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12634587	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12635925	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1357290	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3772107	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772108	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4396926	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56701784	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56875789	0.81[ASN][1000 genomes]
rs57987393	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58297632	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58568267	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs58845625	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59289255	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59708858	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs60167422	0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs61254593	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs61588443	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66935510	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs67199839	0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs72611187	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72611188	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72611189	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72611190	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73212156	0.85[ASN][1000 genomes]
rs7635355	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs939885	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759213	chr3:195102787-196071593	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	esv2757913	chr3:195379484-196071593	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
3	nsv532213	chr3:195643944-196063636	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
4	nsv997797	chr3:195658360-196212958	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
5	nsv432543	chr3:195746690-196015690	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
6	nsv1009811	chr3:195851796-196138071	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
7	nsv461131	chr3:195858887-196072442	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
8	nsv593071	chr3:195858887-196072442	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
9	nsv1009178	chr3:195864466-196081670	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
10	nsv536892	chr3:195864466-196081670	Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
11	nsv1003550	chr3:195885340-196159824	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
12	nsv536893	chr3:195885340-196159824	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
13	nsv878179	chr3:195929268-196019680	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
14	nsv1014563	chr3:195934010-196085951	Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
15	nsv878180	chr3:195946535-196066569	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
16	nsv878181	chr3:195946535-196072442	Enhancers Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
17	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
18	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
19	nsv878182	chr3:195974181-196228360	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7617236	TCTEX1D2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:195965800-196012400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:195969600-196012400	Weak transcription	Fetal Brain Male	brain
3	chr3:195974800-196005000	Weak transcription	Stomach Mucosa	stomach
4	chr3:195984800-196005000	Weak transcription	Fetal Heart	heart
5	chr3:195990400-196006400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:195991800-196012400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr3:195993000-196005200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr3:195995400-196005200	Weak transcription	A549	lung
9	chr3:195996200-196005200	Weak transcription	HUVEC	blood vessel
10	chr3:195996600-196006200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr3:195996600-196012600	Weak transcription	Fetal Kidney	kidney
12	chr3:195997400-196006200	Weak transcription	HSMM	muscle
13	chr3:195997400-196006400	Weak transcription	Brain Angular Gyrus	brain
14	chr3:195997600-196001200	Weak transcription	Brain Anterior Caudate	brain
15	chr3:195997600-196001400	Weak transcription	NH-A	brain
16	chr3:195997600-196001600	Weak transcription	HMEC	breast
17	chr3:195997600-196007800	Weak transcription	Small Intestine	intestine
18	chr3:195997600-196010600	Weak transcription	Colon Smooth Muscle	Colon
19	chr3:195997800-196005000	Weak transcription	NHDF-Ad	bronchial
20	chr3:195997800-196006200	Weak transcription	Brain Hippocampus Middle	brain
21	chr3:195998000-196001400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:195998400-196005000	Weak transcription	Hela-S3	cervix
23	chr3:195999200-196000800	Genic enhancers	Primary T cells fromperipheralblood	blood
24	chr3:195999400-196000600	Genic enhancers	Primary B cells from peripheral blood	blood
25	chr3:195999400-196000600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr3:195999400-196000600	Strong transcription	Colonic Mucosa	Colon
27	chr3:195999400-196000600	Genic enhancers	GM12878-XiMat	blood
28	chr3:195999400-196000600	Strong transcription	Osteobl	bone
29	chr3:195999400-196001000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr3:195999400-196001000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr3:195999400-196001000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr3:195999400-196001000	Genic enhancers	Left Ventricle	heart
33	chr3:195999400-196001400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr3:195999400-196001400	Genic enhancers	Fetal Muscle Leg	muscle
35	chr3:195999400-196001800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr3:195999600-196000600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:195999600-196000600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr3:195999600-196000600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
39	chr3:195999600-196000600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr3:195999600-196000600	Strong transcription	Muscle Satellite Cultured Cells	--
41	chr3:195999600-196000600	Strong transcription	Fetal Brain Female	brain
42	chr3:195999600-196000600	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
43	chr3:195999600-196000600	Strong transcription	Stomach Smooth Muscle	stomach
44	chr3:195999600-196000800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr3:195999600-196000800	Strong transcription	Adipose Nuclei	Adipose
46	chr3:195999600-196000800	ZNF genes & repeats	Brain Germinal Matrix	brain
47	chr3:195999600-196001000	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
48	chr3:195999600-196001000	Strong transcription	Primary B cells from cord blood	blood
49	chr3:195999600-196001000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr3:195999600-196001000	Enhancers	Primary T helper cells PMA-I stimulated	--

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