Variant report

Variant	rs2329462
Chromosome Location	chr7:39644898-39644899
allele	G/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	STAT3	chr7:39644756-39644929	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr7:39644755-39645008	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr7:39644754-39645019	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr7:39644894-39645082	Hela-S3	cervix:	n/a	n/a
5	FOS	chr7:39644730-39645027	MCF10A-Er-Src	breast:	n/a	n/a
6	RUNX3	chr7:39644622-39645019	GM12878	blood:	n/a	n/a
7	FOS	chr7:39644716-39645050	MCF10A-Er-Src	breast:	n/a	n/a
8	RUNX3	chr7:39644690-39644930	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:39642317..39645225-chr7:39656160..39658184,2	MCF-7	breast:
2	chr7:39643975..39649260-chr7:39661579..39666438,6	K562	blood:
3	chr7:39640592..39642673-chr7:39644409..39647009,2	K562	blood:
4	chr7:39643975..39646348-chr7:39661579..39664353,2	K562	blood:

Variant related genes	Relation type
ENSG00000106540	TF binding region
ENSG00000006451	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10245247	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10258946	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10266149	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10486798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10486800	1.00[CEU][hapmap]
rs11983705	0.80[AFR][1000 genomes]
rs11983755	0.80[AFR][1000 genomes]
rs12111908	1.00[ASN][1000 genomes]
rs17171603	0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs17416652	1.00[CEU][hapmap]
rs17507685	1.00[CEU][hapmap]
rs17507748	1.00[CEU][hapmap]
rs17508696	1.00[CEU][hapmap]
rs17713754	0.84[ASN][1000 genomes]
rs17713951	0.88[ASN][1000 genomes]
rs17714049	1.00[ASN][1000 genomes]
rs17770594	0.84[ASN][1000 genomes]
rs17770612	0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs17770625	0.84[ASN][1000 genomes]
rs1989533	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2329455	0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs2329459	0.81[AFR][1000 genomes]
rs2329460	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2329461	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329463	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2876859	0.80[AFR][1000 genomes]
rs4236361	0.80[AFR][1000 genomes]
rs4236363	0.80[AFR][1000 genomes]
rs4451213	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4469364	0.92[AFR][1000 genomes]
rs4720329	0.94[AFR][1000 genomes]
rs4723881	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4723883	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4723884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4723885	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58299139	0.84[ASN][1000 genomes]
rs59071947	0.84[ASN][1000 genomes]
rs61493712	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6958662	0.95[AFR][1000 genomes]
rs6968742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73375695	0.84[ASN][1000 genomes]
rs73379304	0.80[AFR][1000 genomes]
rs7777173	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7785964	0.84[ASN][1000 genomes]
rs7796063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7807233	1.00[CEU][hapmap]
rs7809088	0.95[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv887970	chr7:39587912-39688152	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39632600-39646000	Weak transcription	K562	blood
2	chr7:39638400-39646400	Weak transcription	Stomach Mucosa	stomach
3	chr7:39640400-39645400	Enhancers	HSMM	muscle
4	chr7:39642200-39648200	Weak transcription	NH-A	brain
5	chr7:39642400-39647800	Weak transcription	NHDF-Ad	bronchial
6	chr7:39642400-39647800	Weak transcription	Osteobl	bone
7	chr7:39642400-39648000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr7:39642600-39648600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr7:39643000-39648400	Enhancers	HUVEC	blood vessel
10	chr7:39643400-39645200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr7:39643400-39645400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr7:39643400-39649000	Enhancers	Primary T cells from cord blood	blood
13	chr7:39643800-39645200	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr7:39643800-39645200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr7:39643800-39647000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr7:39643800-39649200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr7:39644000-39645000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr7:39644000-39645200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr7:39644000-39645600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr7:39644000-39646200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr7:39644000-39648000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr7:39644000-39648600	Enhancers	HMEC	breast
23	chr7:39644400-39649000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr7:39644600-39645200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
25	chr7:39644600-39645200	Enhancers	A549	lung
26	chr7:39644600-39645400	Enhancers	Muscle Satellite Cultured Cells	--
27	chr7:39644600-39645400	Enhancers	Small Intestine	intestine
28	chr7:39644600-39646800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr7:39644600-39649000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr7:39644600-39649000	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr7:39644600-39649000	Enhancers	NHEK	skin
32	chr7:39644800-39645200	Enhancers	HSMMtube	muscle
33	chr7:39644800-39645200	Enhancers	NHLF	lung
34	chr7:39644800-39645400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr7:39644800-39645400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr7:39644800-39649800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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