Variant report

Variant	rs6738680
Chromosome Location	chr2:153024113-153024114
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:153023103..153025795-chr2:153030743..153032698,4	K562	blood:
2	chr2:153023722..153029811-chr2:153030516..153033804,9	MCF-7	breast:
3	chr2:153023910..153026125-chr2:153032784..153034657,2	K562	blood:

Variant related genes	Relation type
ENSG00000115145	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10200655	0.86[CHB][hapmap]
rs10427181	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10803936	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs10803938	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs10930910	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs10930913	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs10930916	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10930958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12328066	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12465272	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs12466663	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12467850	0.90[EUR][1000 genomes]
rs12474703	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12617139	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12617696	0.86[CHB][hapmap]
rs12693269	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12995261	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs13000396	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13009432	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs13027217	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs1401778	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs17326047	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs17326118	1.00[JPT][hapmap]
rs17326628	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17326677	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17398329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17398559	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17398585	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1879136	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs1962276	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2345638	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs2345639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2345648	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2345650	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2345895	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2345896	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2345898	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2881245	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35195960	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35594562	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35820971	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3768650	0.86[CHB][hapmap]
rs3820702	0.86[CHB][hapmap]
rs4274558	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4305274	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4664078	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4664536	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55677048	0.90[EUR][1000 genomes]
rs55837285	0.90[EUR][1000 genomes]
rs56018021	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56118729	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56127412	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56888625	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57542496	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62174961	0.90[EUR][1000 genomes]
rs62176480	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62176518	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62176559	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62177360	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62177369	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6433779	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs6650771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6730115	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6731625	0.96[CEU][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6732917	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6740224	0.86[CHB][hapmap]
rs6741737	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs6742259	1.00[CEU][hapmap]
rs6754105	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72857747	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72864757	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7557426	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7579071	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7582231	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs7592014	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7600282	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs7603232	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[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	nsv1005746	chr2:152361972-153059840	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv535984	chr2:152361972-153059840	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv875287	chr2:152714680-153110573	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv875288	chr2:152716628-153183646	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv875289	chr2:152720030-153183646	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	esv1847028	chr2:152863856-153045036	Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv1004308	chr2:152980087-153154534	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv535985	chr2:152980087-153154534	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv459740	chr2:152986041-153045036	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats 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	18 gene(s)	inside rSNPs	diseases
10	nsv583316	chr2:152986041-153045036	Bivalent/Poised TSS ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
11	esv3693434	chr2:152998467-153208713	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 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	chr2:152981800-153024800	Weak transcription	Brain Substantia Nigra	brain
2	chr2:153000200-153031000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:153002800-153030400	Weak transcription	Thymus	Thymus
4	chr2:153003200-153028400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr2:153003600-153028000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:153005200-153028000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr2:153005200-153028200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:153007200-153028200	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr2:153008800-153028800	Weak transcription	Esophagus	oesophagus
10	chr2:153014000-153028400	Weak transcription	Right Ventricle	heart
11	chr2:153014200-153028400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:153014200-153028400	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr2:153015400-153030200	Weak transcription	Primary T cells from cord blood	blood
14	chr2:153017000-153030200	Weak transcription	Fetal Stomach	stomach
15	chr2:153021200-153030600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr2:153021400-153025000	Enhancers	Ovary	ovary
17	chr2:153021400-153028200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr2:153021800-153024200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr2:153022000-153024400	Enhancers	Small Intestine	intestine
20	chr2:153022200-153024400	Enhancers	Liver	Liver
21	chr2:153022200-153031400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:153022400-153024200	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr2:153022400-153024200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr2:153022400-153024200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:153022600-153025400	Enhancers	A549	lung
26	chr2:153022600-153028600	Weak transcription	Right Atrium	heart
27	chr2:153022600-153028800	Weak transcription	Spleen	Spleen
28	chr2:153022800-153025800	Weak transcription	Lung	lung
29	chr2:153022800-153025800	Weak transcription	Pancreas	Pancrea
30	chr2:153022800-153026200	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr2:153022800-153028400	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr2:153022800-153031200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr2:153022800-153031200	Weak transcription	Gastric	stomach
34	chr2:153022800-153031200	Weak transcription	Left Ventricle	heart
35	chr2:153023000-153024200	Enhancers	Brain Angular Gyrus	brain
36	chr2:153023000-153024200	Enhancers	Fetal Lung	lung
37	chr2:153023000-153025000	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr2:153023000-153026400	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr2:153023200-153025400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
40	chr2:153023400-153024200	Flanking Active TSS	Primary hematopoietic stem cells	blood
41	chr2:153023400-153024200	Enhancers	HepG2	liver
42	chr2:153023400-153026400	Enhancers	Brain Hippocampus Middle	brain
43	chr2:153023400-153030400	Weak transcription	Fetal Muscle Leg	muscle
44	chr2:153023400-153030800	Weak transcription	Primary B cells from cord blood	blood
45	chr2:153023600-153024200	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr2:153023600-153024200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr2:153023600-153024200	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr2:153023600-153024200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr2:153023600-153024200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
50	chr2:153023600-153024200	Enhancers	Duodenum Mucosa	Duodenum

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