Variant report

Variant	rs6540901
Chromosome Location	chr1:215810420-215810421
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:215800499..215802863-chr1:215807797..215810435,2	K562	blood:
2	chr1:215800801..215802863-chr1:215808935..215811230,2	K562	blood:
3	chr1:215804655..215806632-chr1:215809197..215810789,2	MCF-7	breast:
4	chr1:215807396..215810772-chr1:215814158..215815812,3	MCF-7	breast:

Extended variants
information (count: 118 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs10127809	0.81[ASN][1000 genomes]
rs11120588	0.92[ASN][1000 genomes]
rs11120591	0.92[ASN][1000 genomes]
rs12089271	0.92[ASN][1000 genomes]
rs1557172	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1819740	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2677113	1.00[CEU][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs2797240	1.00[MEX][hapmap]
rs2797392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3753837	1.00[CEU][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs3753838	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs3767251	1.00[ASN][1000 genomes]
rs3767252	1.00[ASN][1000 genomes]
rs3767253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3767256	0.96[ASN][1000 genomes]
rs3767258	1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3767259	0.96[ASN][1000 genomes]
rs3767260	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs3767262	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs41304083	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41308435	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41315587	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4607849	0.81[ASN][1000 genomes]
rs56783105	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56956076	0.92[ASN][1000 genomes]
rs56957283	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57179404	0.89[ASN][1000 genomes]
rs57311096	1.00[ASN][1000 genomes]
rs57397989	1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs57563355	0.96[ASN][1000 genomes]
rs57628126	0.92[ASN][1000 genomes]
rs57758604	0.92[ASN][1000 genomes]
rs57861859	0.96[ASN][1000 genomes]
rs57935471	0.96[ASN][1000 genomes]
rs58102262	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs58162887	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58257972	1.00[ASN][1000 genomes]
rs58330534	0.92[ASN][1000 genomes]
rs58425452	0.92[ASN][1000 genomes]
rs58542168	1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs58557470	0.92[ASN][1000 genomes]
rs58594611	1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs58597977	0.92[ASN][1000 genomes]
rs58629829	0.92[ASN][1000 genomes]
rs58649725	1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs58682085	0.96[ASN][1000 genomes]
rs58759277	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58836680	0.92[ASN][1000 genomes]
rs58867901	0.96[ASN][1000 genomes]
rs58919310	0.92[ASN][1000 genomes]
rs59015398	0.96[ASN][1000 genomes]
rs59026507	0.96[ASN][1000 genomes]
rs59040705	0.92[ASN][1000 genomes]
rs59192192	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59233975	0.92[ASN][1000 genomes]
rs59319848	1.00[ASN][1000 genomes]
rs59577074	0.84[ASN][1000 genomes]
rs59635576	1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs59636344	0.96[ASN][1000 genomes]
rs60365921	0.92[ASN][1000 genomes]
rs60404320	0.84[ASN][1000 genomes]
rs60533889	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60590154	1.00[ASN][1000 genomes]
rs60620576	0.81[ASN][1000 genomes]
rs61368758	0.92[ASN][1000 genomes]
rs61502956	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61522423	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61600848	0.81[ASN][1000 genomes]
rs61633090	0.92[ASN][1000 genomes]
rs61685588	0.92[ASN][1000 genomes]
rs6667509	1.00[JPT][hapmap]
rs6676725	1.00[ASW][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.82[YRI][hapmap]
rs6689680	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6700397	1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs73081443	0.92[ASN][1000 genomes]
rs73081447	0.92[ASN][1000 genomes]
rs73081459	0.92[ASN][1000 genomes]
rs73081470	0.92[ASN][1000 genomes]
rs73081479	0.92[ASN][1000 genomes]
rs73081487	0.92[ASN][1000 genomes]
rs73081497	0.92[ASN][1000 genomes]
rs73083403	0.85[ASN][1000 genomes]
rs73083410	0.92[ASN][1000 genomes]
rs73083415	0.92[ASN][1000 genomes]
rs73083420	0.92[ASN][1000 genomes]
rs73083421	1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs73083429	1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs73083436	1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs73083437	1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs73083461	1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs73083470	1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs73083500	0.96[ASN][1000 genomes]
rs73085404	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs73085410	1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs73087423	1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs73087440	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73087444	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73087448	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73087450	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73087454	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73087457	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73087461	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73087467	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73091998	0.81[ASN][1000 genomes]
rs73094106	0.81[ASN][1000 genomes]
rs73094120	0.92[ASN][1000 genomes]
rs73094142	0.89[ASN][1000 genomes]
rs73100105	0.92[ASN][1000 genomes]
rs73100108	0.92[ASN][1000 genomes]
rs73100110	0.92[ASN][1000 genomes]
rs73100116	0.92[ASN][1000 genomes]
rs73100129	0.92[ASN][1000 genomes]
rs73100141	0.92[ASN][1000 genomes]
rs7522198	0.84[ASW][hapmap];1.00[YRI][hapmap]
rs7522720	1.00[YRI][hapmap]
rs7531580	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7545425	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.96[ASN][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	nsv430324	chr1:215649163-216082605	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:215805000-215811000	Enhancers	Fetal Intestine Large	intestine
2	chr1:215806000-215813600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:215807600-215811000	Enhancers	Fetal Intestine Small	intestine
4	chr1:215809200-215810600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:215809200-215810600	Enhancers	Gastric	stomach
6	chr1:215809400-215810600	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr1:215809400-215810600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:215809400-215810600	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr1:215809400-215810600	Enhancers	Placenta	Placenta
10	chr1:215809400-215810800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:215809400-215810800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:215809400-215811000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:215809400-215811000	Flanking Active TSS	HepG2	liver
14	chr1:215809600-215810600	Enhancers	H1 Cell Line	embryonic stem cell
15	chr1:215809600-215810600	Enhancers	Fetal Lung	lung
16	chr1:215809600-215810800	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr1:215809600-215810800	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr1:215809600-215811000	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr1:215809600-215811000	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr1:215809600-215811000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:215809600-215811000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:215809800-215810600	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr1:215809800-215810600	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr1:215809800-215810600	Flanking Active TSS	NHDF-Ad	bronchial
25	chr1:215809800-215810800	Enhancers	H9 Cell Line	embryonic stem cell
26	chr1:215809800-215810800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr1:215809800-215810800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:215809800-215810800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
29	chr1:215809800-215810800	Enhancers	Pancreas	Pancrea
30	chr1:215809800-215811000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr1:215809800-215811000	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr1:215809800-215811000	Flanking Active TSS	Duodenum Mucosa	Duodenum
33	chr1:215809800-215811000	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr1:215809800-215811000	Flanking Active TSS	Osteobl	bone
35	chr1:215809800-215811800	Enhancers	Stomach Mucosa	stomach
36	chr1:215810000-215810600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:215810000-215810600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
38	chr1:215810000-215810600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
39	chr1:215810000-215810800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr1:215810000-215810800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:215810000-215810800	Flanking Active TSS	Adipose Nuclei	Adipose
42	chr1:215810000-215810800	Flanking Active TSS	Liver	Liver
43	chr1:215810000-215810800	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr1:215810200-215810600	Active TSS	Brain Anterior Caudate	brain
45	chr1:215810200-215810600	Active TSS	Brain Inferior Temporal Lobe	brain
46	chr1:215810200-215810600	Flanking Active TSS	Colonic Mucosa	Colon
47	chr1:215810200-215810600	Enhancers	Left Ventricle	heart
48	chr1:215810200-215810600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
49	chr1:215810200-215810600	Enhancers	Small Intestine	intestine
50	chr1:215810200-215810600	Flanking Active TSS	Stomach Smooth Muscle	stomach

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