Variant report

Variant	rs6728189
Chromosome Location	chr2:153557883-153557884
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:153555340..153556885-chr2:153557265..153559001,2	MCF-7	breast:
2	chr2:153554769..153561611-chr2:153571715..153575304,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177917	Chromatin interaction
ENSG00000196504	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10497113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10931263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10931271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10931279	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1135617	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11674911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11676069	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11694512	0.84[ASN][1000 genomes]
rs11901227	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12475871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12478681	0.84[ASN][1000 genomes]
rs12693429	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs12989903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12990935	1.00[CHB][hapmap]
rs12995388	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12999331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13003670	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13006652	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13014141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13017131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13022436	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13023779	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13023975	0.84[EUR][1000 genomes]
rs1370499	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16831440	0.84[EUR][1000 genomes]
rs16831456	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17328776	1.00[CHB][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17400456	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17400938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17400952	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17400980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2083097	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2346551	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34199006	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34454505	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34469468	0.84[EUR][1000 genomes]
rs34619076	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34775858	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35002744	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35421285	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35754252	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35894330	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35937874	0.93[EUR][1000 genomes]
rs36107565	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36122595	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3811568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3811569	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4575677	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6434172	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66492085	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66849546	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6736003	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs71417232	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs71417235	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72871148	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7591590	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7598878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834421	chr2:153470109-153664235	Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv3693438	chr2:153505376-153718246	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153518800-153558000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:153523400-153571800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:153525000-153571800	Weak transcription	Small Intestine	intestine
4	chr2:153533200-153558000	Weak transcription	Colonic Mucosa	Colon
5	chr2:153533400-153558600	Weak transcription	Aorta	Aorta
6	chr2:153533400-153571600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr2:153533800-153558000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr2:153533800-153572600	Weak transcription	Fetal Brain Male	brain
9	chr2:153536000-153572600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr2:153537400-153565400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr2:153537600-153558400	Weak transcription	Fetal Brain Female	brain
12	chr2:153537600-153571800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr2:153539600-153571800	Weak transcription	Brain Anterior Caudate	brain
14	chr2:153539600-153572400	Weak transcription	Brain Angular Gyrus	brain
15	chr2:153539600-153572400	Weak transcription	Pancreas	Pancrea
16	chr2:153544400-153568200	Weak transcription	Fetal Kidney	kidney
17	chr2:153550600-153558000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr2:153550800-153558000	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr2:153550800-153558000	Weak transcription	Fetal Muscle Trunk	muscle
20	chr2:153551000-153558000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr2:153551200-153558000	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr2:153551200-153558000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr2:153551200-153558000	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr2:153551200-153558000	Weak transcription	Fetal Muscle Leg	muscle
25	chr2:153551200-153558200	Weak transcription	Left Ventricle	heart
26	chr2:153551200-153558400	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr2:153551200-153560200	Weak transcription	Psoas Muscle	Psoas
28	chr2:153551200-153561200	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr2:153551200-153562800	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr2:153551200-153563400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr2:153551200-153567200	Weak transcription	Hela-S3	cervix
32	chr2:153551200-153568000	Weak transcription	Ovary	ovary
33	chr2:153551200-153571400	Weak transcription	Brain Hippocampus Middle	brain
34	chr2:153551200-153571800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr2:153551200-153571800	Weak transcription	Brain Substantia Nigra	brain
36	chr2:153551200-153572400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr2:153551400-153558000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr2:153551400-153562200	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr2:153551400-153563000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr2:153551400-153566400	Weak transcription	HUVEC	blood vessel
41	chr2:153551400-153568400	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr2:153551400-153571800	Weak transcription	HSMMtube	muscle
43	chr2:153551600-153558200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr2:153552400-153567400	Weak transcription	Colon Smooth Muscle	Colon
45	chr2:153552600-153559600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr2:153554000-153558200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr2:153554000-153558800	Weak transcription	Fetal Heart	heart
48	chr2:153554200-153558000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr2:153554200-153566800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr2:153554400-153558000	Weak transcription	Primary hematopoietic stem cells	blood

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