Variant report

Variant	rs10739378
Chromosome Location	chr9:115639631-115639632
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:115637754..115639637-chr9:115650697..115653230,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119457	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10114602	0.87[EUR][1000 genomes]
rs10114623	0.87[EUR][1000 genomes]
rs10115576	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs10115711	0.82[CEU][hapmap]
rs10116897	0.87[EUR][1000 genomes]
rs10124260	0.85[CEU][hapmap]
rs10124939	0.82[CEU][hapmap];1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs10124979	0.82[CEU][hapmap]
rs1041086	0.94[EUR][1000 genomes]
rs10733594	0.85[CEU][hapmap]
rs10733598	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs10733599	1.00[CEU][hapmap]
rs10739370	0.82[CEU][hapmap]
rs10739373	0.85[CEU][hapmap]
rs10739376	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs10739377	0.87[EUR][1000 genomes]
rs10739379	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739380	0.89[ASN][1000 genomes]
rs10759590	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs10759603	1.00[CEU][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10759604	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10981534	0.87[EUR][1000 genomes]
rs1324930	0.87[EUR][1000 genomes]
rs1324931	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs1324932	0.87[EUR][1000 genomes]
rs1361720	0.85[CEU][hapmap]
rs1418409	0.85[CEU][hapmap]
rs1475293	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs1539338	0.85[CEU][hapmap]
rs1891402	0.85[CEU][hapmap]
rs1891403	0.85[CEU][hapmap]
rs2025544	1.00[CEU][hapmap]
rs2645993	0.85[CEU][hapmap]
rs2796028	0.85[CEU][hapmap]
rs4246892	0.85[CEU][hapmap]
rs4304397	0.85[CEU][hapmap]
rs4978507	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs4978509	0.87[EUR][1000 genomes]
rs4978511	0.82[CEU][hapmap];1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs4979153	0.85[CEU][hapmap]
rs4979154	0.85[CEU][hapmap]
rs4979157	0.85[CEU][hapmap]
rs4979165	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs4979170	1.00[CEU][hapmap];0.94[YRI][hapmap];0.94[EUR][1000 genomes]
rs4979173	0.94[EUR][1000 genomes]
rs4979175	0.87[EUR][1000 genomes]
rs4979176	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4979177	0.92[EUR][1000 genomes]
rs4979178	0.92[EUR][1000 genomes]
rs62576453	0.86[EUR][1000 genomes]
rs6477959	0.85[CEU][hapmap]
rs700122	0.85[CEU][hapmap]
rs7023956	0.82[EUR][1000 genomes]
rs7030795	0.85[CEU][hapmap]
rs7047914	0.92[EUR][1000 genomes]
rs7859175	0.85[CEU][hapmap]
rs7868830	0.85[CEU][hapmap]
rs787271	0.85[CEU][hapmap]
rs787276	0.85[CEU][hapmap]
rs787280	0.85[CEU][hapmap]
rs787284	0.85[CEU][hapmap]
rs787287	0.85[CEU][hapmap]
rs787294	0.85[CEU][hapmap]
rs787295	0.85[CEU][hapmap]
rs787297	0.85[CEU][hapmap]
rs787298	0.85[CEU][hapmap]
rs787299	0.85[CEU][hapmap]
rs787301	0.85[CEU][hapmap]
rs787302	0.85[CEU][hapmap]
rs7873289	1.00[CEU][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs813101	0.85[CEU][hapmap]
rs885387	0.85[CEU][hapmap]
rs9409123	0.85[CEU][hapmap]

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	esv2758198	chr9:115240454-116002951	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription 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	57 gene(s)	inside rSNPs	diseases
2	esv2759710	chr9:115240454-116002951	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv893733	chr9:115397206-115712068	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	esv2422302	chr9:115550339-115656433	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv1047000	chr9:115610445-115884038	ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115601200-115641200	Weak transcription	Fetal Brain Male	brain
2	chr9:115607400-115643400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr9:115613600-115642600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr9:115615600-115646400	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr9:115624200-115652600	Weak transcription	Fetal Heart	heart
6	chr9:115625800-115645200	Weak transcription	Thymus	Thymus
7	chr9:115626400-115650800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr9:115627000-115647000	Weak transcription	Colonic Mucosa	Colon
9	chr9:115627600-115642000	Weak transcription	Primary hematopoietic stem cells	blood
10	chr9:115627600-115646800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr9:115627800-115640600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr9:115628600-115640800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr9:115630600-115642000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr9:115630600-115643400	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr9:115630600-115646400	Weak transcription	Fetal Lung	lung
16	chr9:115630600-115647200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr9:115630800-115643400	Weak transcription	NHEK	skin
18	chr9:115630800-115643600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr9:115630800-115643600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr9:115630800-115646400	Weak transcription	Placenta	Placenta
21	chr9:115631200-115643600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr9:115631200-115646400	Weak transcription	Fetal Kidney	kidney
23	chr9:115631400-115643800	Weak transcription	Colon Smooth Muscle	Colon
24	chr9:115631600-115642800	Weak transcription	Ovary	ovary
25	chr9:115631800-115642800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr9:115631800-115642800	Weak transcription	HSMM	muscle
27	chr9:115631800-115646400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr9:115631800-115652200	Weak transcription	Gastric	stomach
29	chr9:115632000-115642600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr9:115632200-115644800	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr9:115632400-115643200	Weak transcription	HSMMtube	muscle
32	chr9:115632600-115641000	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr9:115632800-115639800	Weak transcription	Brain Germinal Matrix	brain
34	chr9:115632800-115643400	Weak transcription	HMEC	breast
35	chr9:115633000-115645800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr9:115633000-115646400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr9:115633000-115652600	Weak transcription	Left Ventricle	heart
38	chr9:115633200-115641200	Weak transcription	HepG2	liver
39	chr9:115633200-115642800	Weak transcription	Brain Anterior Caudate	brain
40	chr9:115633200-115646400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr9:115633200-115652400	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr9:115633200-115652400	Weak transcription	Right Ventricle	heart
43	chr9:115633400-115643400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr9:115633400-115643600	Weak transcription	Pancreas	Pancrea
45	chr9:115633400-115646800	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr9:115633400-115648200	Weak transcription	Esophagus	oesophagus
47	chr9:115633400-115649200	Weak transcription	Duodenum Mucosa	Duodenum
48	chr9:115633600-115644400	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr9:115633800-115640400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr9:115633800-115641600	Weak transcription	Brain Substantia Nigra	brain

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