Variant report

Variant	rs3798604
Chromosome Location	chr6:119517327-119517328
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:119506495..119510474-chr6:119512105..119518415,7	K562	blood:
2	chr6:119510956..119512728-chr6:119517254..119518808,2	MCF-7	breast:

Extended variants
information (count: 109 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10484999	1.00[AFR][1000 genomes]
rs10485000	1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs10485002	1.00[AFR][1000 genomes]
rs1342312	1.00[AFR][1000 genomes]
rs17052761	1.00[AFR][1000 genomes]
rs17080912	1.00[JPT][hapmap]
rs17080956	1.00[AFR][1000 genomes]
rs17080961	1.00[AFR][1000 genomes]
rs17080974	1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs17080980	1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs17080995	1.00[ASW][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs17081016	1.00[AFR][1000 genomes]
rs17081019	1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs17081022	1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs17081026	1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs17081029	1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs17081031	1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs17081044	1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs17441889	1.00[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs17441930	1.00[MEX][hapmap]
rs17442112	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17442126	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17442140	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17442147	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17442154	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17442182	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17442343	1.00[CEU][hapmap]
rs17513883	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17513904	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17536339	1.00[CEU][hapmap]
rs17619366	1.00[CEU][hapmap]
rs2299885	1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs28364695	1.00[AFR][1000 genomes]
rs3756942	1.00[ASW][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3765248	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3778105	1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs3778106	1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs3778108	1.00[AFR][1000 genomes]
rs3778109	1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs3798606	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs3798607	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs3798611	1.00[AFR][1000 genomes]
rs3798615	1.00[AFR][1000 genomes]
rs3798617	1.00[AFR][1000 genomes]
rs3798625	1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs3798626	1.00[AFR][1000 genomes]
rs3798627	1.00[AFR][1000 genomes]
rs3798628	1.00[AFR][1000 genomes]
rs3798629	1.00[AFR][1000 genomes]
rs3798630	1.00[AFR][1000 genomes]
rs3798632	1.00[JPT][hapmap]
rs3798633	1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs3798634	1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs3798635	1.00[AFR][1000 genomes]
rs3798637	1.00[AFR][1000 genomes]
rs3798638	1.00[AFR][1000 genomes]
rs3798639	1.00[AFR][1000 genomes]
rs3798640	1.00[AFR][1000 genomes]
rs3798641	1.00[AFR][1000 genomes]
rs3798642	1.00[AFR][1000 genomes]
rs3798643	1.00[AFR][1000 genomes]
rs3798645	1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs3798646	1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs3798647	1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs3798656	1.00[AFR][1000 genomes]
rs3823001	1.00[AFR][1000 genomes]
rs3823004	1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs3823005	1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs57114522	1.00[AFR][1000 genomes]
rs57560532	1.00[AFR][1000 genomes]
rs57606082	1.00[AFR][1000 genomes]
rs57900721	1.00[AFR][1000 genomes]
rs57980534	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs58263645	1.00[AFR][1000 genomes]
rs58928989	1.00[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs59771009	1.00[AFR][1000 genomes]
rs60924800	1.00[AFR][1000 genomes]
rs60944461	1.00[AFR][1000 genomes]
rs61362597	1.00[AFR][1000 genomes]
rs61399235	1.00[AFR][1000 genomes]
rs61534068	1.00[AFR][1000 genomes]
rs6569052	1.00[AFR][1000 genomes]
rs6900434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6901117	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6901238	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6918093	1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs6922532	1.00[AFR][1000 genomes]
rs6922683	1.00[AFR][1000 genomes]
rs6922722	1.00[AFR][1000 genomes]
rs6922867	1.00[AFR][1000 genomes]
rs6923320	1.00[AFR][1000 genomes]
rs6923365	1.00[AFR][1000 genomes]
rs6923550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6923755	1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs6926266	1.00[CEU][hapmap]
rs6929286	1.00[AFR][1000 genomes]
rs6940750	1.00[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6941142	1.00[CEU][hapmap]
rs7745631	1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs7748940	1.00[CEU][hapmap]
rs947589	1.00[AFR][1000 genomes]
rs9481896	1.00[CEU][hapmap]
rs9489641	1.00[CEU][hapmap]
rs9489642	1.00[CEU][hapmap]
rs9489647	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025995	chr6:119407742-119709548	Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv886570	chr6:119450888-119600556	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1017507	chr6:119465981-119664949	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1034992	chr6:119512657-119540895	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119491800-119531200	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr6:119492200-119527800	Weak transcription	NHEK	skin
3	chr6:119492400-119524200	Weak transcription	Fetal Stomach	stomach
4	chr6:119493600-119518000	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr6:119494000-119523600	Weak transcription	GM12878-XiMat	blood
6	chr6:119494600-119547400	Weak transcription	Esophagus	oesophagus
7	chr6:119494800-119526200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr6:119495400-119522000	Weak transcription	Colon Smooth Muscle	Colon
9	chr6:119495600-119522200	Weak transcription	Fetal Kidney	kidney
10	chr6:119497000-119524000	Weak transcription	NHLF	lung
11	chr6:119497000-119524400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr6:119497000-119524400	Weak transcription	Small Intestine	intestine
13	chr6:119497200-119518600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr6:119498000-119536600	Weak transcription	Fetal Heart	heart
15	chr6:119498200-119527400	Strong transcription	Liver	Liver
16	chr6:119498600-119517600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr6:119498600-119531400	Strong transcription	HepG2	liver
18	chr6:119498800-119526800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr6:119499400-119518200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr6:119499400-119525400	Weak transcription	NH-A	brain
21	chr6:119499600-119524000	Weak transcription	Brain Anterior Caudate	brain
22	chr6:119499800-119524400	Weak transcription	Right Ventricle	heart
23	chr6:119501200-119522200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr6:119501600-119518000	Weak transcription	Thymus	Thymus
25	chr6:119501600-119524200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr6:119502000-119523800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr6:119502000-119523800	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr6:119502400-119525800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr6:119502600-119526800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr6:119503400-119539800	Weak transcription	Gastric	stomach
31	chr6:119503800-119524200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr6:119504600-119519400	Strong transcription	Adipose Nuclei	Adipose
33	chr6:119505200-119527400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr6:119505400-119518800	Weak transcription	Brain Substantia Nigra	brain
35	chr6:119505600-119518600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr6:119505800-119524000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr6:119506800-119530800	Weak transcription	Stomach Mucosa	stomach
38	chr6:119507800-119525000	Weak transcription	Osteobl	bone
39	chr6:119508000-119524000	Weak transcription	Spleen	Spleen
40	chr6:119508200-119518000	Weak transcription	Aorta	Aorta
41	chr6:119508200-119518200	Weak transcription	Lung	lung
42	chr6:119508200-119522000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr6:119508200-119523800	Weak transcription	Ovary	ovary
44	chr6:119508200-119524400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr6:119509200-119518200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr6:119509800-119530000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr6:119510000-119526200	Weak transcription	Brain Angular Gyrus	brain
48	chr6:119510000-119529800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr6:119511000-119524000	Weak transcription	Primary T cells from cord blood	blood
50	chr6:119511200-119530000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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