Variant report

Variant	rs3828857
Chromosome Location	chr6:5666064-5666065
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12174223	1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12190311	1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap]
rs12524821	0.83[ASN][1000 genomes]
rs12662009	0.93[ASN][1000 genomes]
rs3812177	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	nsv916361	chr6:5315853-5695486	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv600887	chr6:5545046-5694713	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5641400-5673800	Weak transcription	Fetal Intestine Small	intestine
2	chr6:5641600-5671400	Weak transcription	Lung	lung
3	chr6:5642200-5672400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:5645400-5666200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:5650000-5671400	Weak transcription	Small Intestine	intestine
6	chr6:5651200-5671400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr6:5653200-5677600	Weak transcription	Gastric	stomach
8	chr6:5654600-5671400	Weak transcription	Left Ventricle	heart
9	chr6:5654600-5677600	Weak transcription	Pancreas	Pancrea
10	chr6:5656000-5672200	Weak transcription	Aorta	Aorta
11	chr6:5656800-5669800	Weak transcription	NHEK	skin
12	chr6:5656800-5670000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr6:5658000-5671400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr6:5660400-5672600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr6:5661200-5672200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr6:5661600-5671400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr6:5662600-5666200	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr6:5663200-5673400	Weak transcription	Fetal Brain Male	brain
19	chr6:5663400-5666200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr6:5663400-5672400	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr6:5663600-5667200	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr6:5663600-5668200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr6:5664000-5668000	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr6:5664000-5668200	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr6:5664000-5670200	Enhancers	Primary T cells fromperipheralblood	blood
26	chr6:5664200-5666200	Enhancers	GM12878-XiMat	blood
27	chr6:5664200-5666800	Enhancers	Primary B cells from peripheral blood	blood
28	chr6:5664200-5670800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr6:5664400-5666800	Enhancers	Thymus	Thymus
30	chr6:5664400-5668600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr6:5664600-5668800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr6:5664800-5667000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr6:5664800-5669600	Enhancers	Dnd41	blood
34	chr6:5664800-5673400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr6:5665200-5668600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr6:5665200-5677800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr6:5665400-5666200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr6:5665400-5667400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
39	chr6:5665600-5666200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr6:5665600-5666600	Flanking Active TSS	Primary T cells from cord blood	blood
41	chr6:5665600-5671400	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr6:5665600-5671600	Weak transcription	Spleen	Spleen
43	chr6:5665800-5666200	Flanking Active TSS	Primary B cells from cord blood	blood
44	chr6:5665800-5666200	Flanking Active TSS	Fetal Thymus	thymus
45	chr6:5665800-5668000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr6:5666000-5666200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr6:5666000-5666200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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