Variant report

Variant	rs4711598
Chromosome Location	chr6:39398097-39398098
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10484825	0.91[YRI][hapmap]
rs10947813	0.90[ASN][1000 genomes]
rs11962587	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11964924	0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11968704	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs11969059	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11969395	0.86[ASN][1000 genomes]
rs1410488	0.86[ASN][1000 genomes]
rs16892158	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs1927774	0.89[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs1927775	0.89[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs1952362	0.89[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs2026670	0.89[CHB][hapmap];0.86[CHD][hapmap]
rs2235817	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs2273063	0.83[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap]
rs2395727	0.86[ASN][1000 genomes]
rs28533484	0.89[ASN][1000 genomes]
rs35553201	0.88[ASN][1000 genomes]
rs3736735	0.86[JPT][hapmap]
rs4236064	0.94[CHB][hapmap];0.94[CHD][hapmap]
rs4464790	0.88[ASN][1000 genomes]
rs4482968	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs4540261	0.84[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap]
rs4714253	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4714254	0.86[ASN][1000 genomes]
rs4714255	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4714256	0.89[CHB][hapmap];0.94[CHD][hapmap]
rs9296298	0.84[CHB][hapmap];0.86[CHD][hapmap]
rs9296299	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9296300	0.84[CHB][hapmap];0.91[CHD][hapmap]
rs9349120	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9357305	0.88[ASN][1000 genomes]
rs9357308	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs9357309	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs9367008	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs9367009	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9367012	0.82[CHB][hapmap];0.93[JPT][hapmap]
rs9369117	0.85[ASN][1000 genomes]
rs9369119	0.84[CHB][hapmap];0.91[CHD][hapmap]
rs9380861	0.95[ASN][1000 genomes]
rs9380862	0.86[ASN][1000 genomes]
rs9380863	0.89[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs9380864	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9380865	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9380867	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs9380868	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs9380873	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs9380877	0.86[JPT][hapmap]
rs9380880	0.82[CHD][hapmap]
rs9394592	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9394594	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9394595	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9394598	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs9394599	0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs9394600	0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9394602	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs9394606	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs9394608	0.86[JPT][hapmap]
rs9394609	0.86[JPT][hapmap]
rs9394611	0.86[JPT][hapmap]
rs9471103	0.86[ASN][1000 genomes]
rs9471113	0.89[CHB][hapmap]

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	nsv830645	chr6:39227601-39408310	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv885822	chr6:39327708-39721216	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39385200-39398800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:39389400-39398200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr6:39390400-39399000	Weak transcription	Stomach Mucosa	stomach
4	chr6:39390600-39398800	Weak transcription	Lung	lung
5	chr6:39394200-39398400	Weak transcription	Colon Smooth Muscle	Colon
6	chr6:39394200-39398800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr6:39394200-39398800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr6:39394200-39399000	Weak transcription	Osteobl	bone
9	chr6:39394400-39398200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr6:39394400-39398400	Weak transcription	Brain Angular Gyrus	brain
11	chr6:39394400-39398600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr6:39394400-39398800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr6:39394400-39398800	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr6:39394400-39399000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr6:39394400-39399000	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr6:39394400-39399000	Weak transcription	NH-A	brain
17	chr6:39394600-39398400	Weak transcription	Brain Hippocampus Middle	brain
18	chr6:39394800-39398400	Weak transcription	Brain Anterior Caudate	brain
19	chr6:39394800-39398400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr6:39395000-39398200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr6:39395000-39398200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr6:39395200-39398600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr6:39395400-39400000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:39396600-39398800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr6:39397000-39398400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr6:39397000-39398800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr6:39397000-39398800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr6:39397000-39399000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr6:39397000-39399200	Weak transcription	NHEK	skin
30	chr6:39397000-39400800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr6:39397000-39401400	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr6:39397000-39401800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr6:39397200-39398200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr6:39397200-39398600	Weak transcription	HMEC	breast
35	chr6:39397200-39400200	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr6:39397400-39401600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr6:39397600-39398400	Enhancers	Brain Substantia Nigra	brain
38	chr6:39397600-39399400	Enhancers	Fetal Lung	lung
39	chr6:39397600-39400600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr6:39397600-39400800	Enhancers	Fetal Muscle Leg	muscle
41	chr6:39397800-39398600	Enhancers	NHDF-Ad	bronchial
42	chr6:39397800-39398800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr6:39397800-39398800	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr6:39397800-39399600	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr6:39397800-39400400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr6:39397800-39400600	Enhancers	Fetal Stomach	stomach
47	chr6:39398000-39399400	Enhancers	Fetal Heart	heart
48	chr6:39398000-39399600	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr6:39398000-39400600	Enhancers	HSMMtube	muscle

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