Variant report

Variant	rs6707902
Chromosome Location	chr2:55491791-55491792
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55462896..55465238-chr2:55491054..55493846,2	MCF-7	breast:
2	chr2:55489175..55493124-chr2:55494672..55498680,8	MCF-7	breast:
3	chr2:55491409..55498987-chr2:55507178..55511380,11	MCF-7	breast:
4	chr2:55490801..55492846-chr2:55494879..55496493,2	K562	blood:
5	chr2:55481797..55485521-chr2:55489463..55492846,3	K562	blood:

Variant related genes	Relation type
ENSG00000162997	Chromatin interaction
ENSG00000085760	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10192809	1.00[EUR][1000 genomes]
rs10209298	1.00[EUR][1000 genomes]
rs11679663	0.88[YRI][hapmap]
rs11886358	1.00[EUR][1000 genomes]
rs11887112	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11888119	1.00[MEX][hapmap]
rs11889466	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11890896	1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11894557	1.00[MEX][hapmap]
rs11896438	1.00[EUR][1000 genomes]
rs11899921	1.00[MEX][hapmap]
rs11902622	1.00[EUR][1000 genomes]
rs12621144	0.92[YRI][hapmap]
rs13012766	0.87[YRI][hapmap]
rs13013134	0.96[YRI][hapmap]
rs13019355	0.90[YRI][hapmap]
rs13399572	1.00[MEX][hapmap]
rs17046771	0.86[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17046787	0.81[ASW][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3935223	0.88[YRI][hapmap]
rs55726603	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55735105	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56219595	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56887573	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56902676	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57489147	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57517202	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58016152	1.00[EUR][1000 genomes]
rs58207828	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58485503	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59832517	0.82[AMR][1000 genomes]
rs60944260	1.00[EUR][1000 genomes]
rs61197615	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6545474	0.83[YRI][hapmap]
rs6545478	0.87[YRI][hapmap]
rs6714830	0.83[YRI][hapmap]
rs6716121	0.80[ASW][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6721728	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6723598	0.92[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6724153	0.92[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6736539	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73936831	1.00[EUR][1000 genomes]
rs73936834	1.00[EUR][1000 genomes]
rs73936837	1.00[EUR][1000 genomes]
rs73936845	1.00[EUR][1000 genomes]
rs73936947	1.00[EUR][1000 genomes]
rs73936949	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73936959	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73936964	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7596403	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7608709	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3348896	chr2:55429540-55498552	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv874156	chr2:55474026-55636351	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv3502708	chr2:55481350-55506212	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	esv3502709	chr2:55481350-55506212	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
6	nsv525025	chr2:55483020-55505456	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	nsv874157	chr2:55483020-55571085	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55461600-55495400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:55461600-55495400	Weak transcription	Stomach Mucosa	stomach
3	chr2:55461800-55493400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr2:55461800-55495000	Weak transcription	Fetal Brain Male	brain
5	chr2:55462000-55493200	Strong transcription	Duodenum Mucosa	Duodenum
6	chr2:55463000-55495400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:55463800-55494800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:55463800-55495600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:55464600-55495800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr2:55465600-55494400	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr2:55466000-55493200	Strong transcription	Rectal Mucosa Donor 31	rectum
12	chr2:55468200-55493400	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr2:55468400-55493200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr2:55468400-55494400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:55468600-55494400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr2:55468800-55493600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr2:55468800-55494400	Strong transcription	Adipose Nuclei	Adipose
18	chr2:55468800-55494400	Strong transcription	Liver	Liver
19	chr2:55469400-55492600	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr2:55470800-55494200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr2:55472000-55495200	Weak transcription	Psoas Muscle	Psoas
22	chr2:55476000-55495400	Weak transcription	HUVEC	blood vessel
23	chr2:55476600-55495400	Weak transcription	Aorta	Aorta
24	chr2:55476600-55495400	Weak transcription	Fetal Heart	heart
25	chr2:55476600-55495600	Weak transcription	Esophagus	oesophagus
26	chr2:55476800-55495400	Weak transcription	Fetal Kidney	kidney
27	chr2:55478400-55493400	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr2:55478400-55494800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:55478800-55494200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr2:55479000-55493400	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr2:55480000-55495400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr2:55480400-55495600	Weak transcription	Brain Substantia Nigra	brain
33	chr2:55481400-55495400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr2:55481400-55495400	Weak transcription	Fetal Lung	lung
35	chr2:55481600-55495400	Weak transcription	NHDF-Ad	bronchial
36	chr2:55482800-55492000	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr2:55482800-55492400	Strong transcription	Left Ventricle	heart
38	chr2:55482800-55494600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr2:55483000-55494400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr2:55483000-55494600	Strong transcription	Fetal Intestine Small	intestine
41	chr2:55483000-55494600	Strong transcription	Fetal Stomach	stomach
42	chr2:55483200-55494800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr2:55483800-55492200	Strong transcription	Fetal Intestine Large	intestine
44	chr2:55484000-55491800	Strong transcription	Primary B cells from peripheral blood	blood
45	chr2:55484000-55493400	Strong transcription	HepG2	liver
46	chr2:55484000-55493600	Strong transcription	Placenta	Placenta
47	chr2:55484600-55492400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr2:55484600-55493400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr2:55484600-55493400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr2:55484600-55494400	Strong transcription	HUES6 Cell Line	embryonic stem cell

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