Variant report

Variant	rs638804
Chromosome Location	chr6:142535138-142535139
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs11758623	0.90[ASN][1000 genomes]
rs178783	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225601	0.83[ASN][1000 genomes]
rs225602	0.83[ASN][1000 genomes]
rs225606	0.83[ASN][1000 genomes]
rs225618	0.85[ASN][1000 genomes]
rs225622	0.85[ASN][1000 genomes]
rs225630	0.85[ASN][1000 genomes]
rs225631	0.85[ASN][1000 genomes]
rs225632	0.85[ASN][1000 genomes]
rs225633	0.85[ASN][1000 genomes]
rs225634	0.85[ASN][1000 genomes]
rs225635	0.85[ASN][1000 genomes]
rs225636	0.85[ASN][1000 genomes]
rs225639	0.85[ASN][1000 genomes]
rs225640	0.85[ASN][1000 genomes]
rs225641	0.85[ASN][1000 genomes]
rs225642	0.85[ASN][1000 genomes]
rs225643	0.85[ASN][1000 genomes]
rs225650	0.90[ASN][1000 genomes]
rs225651	0.90[ASN][1000 genomes]
rs225652	0.90[ASN][1000 genomes]
rs225653	0.88[ASN][1000 genomes]
rs225654	0.90[ASN][1000 genomes]
rs225655	0.90[ASN][1000 genomes]
rs225658	0.90[ASN][1000 genomes]
rs225659	0.88[ASN][1000 genomes]
rs225660	0.90[ASN][1000 genomes]
rs225661	0.87[ASN][1000 genomes]
rs225662	0.90[ASN][1000 genomes]
rs225663	0.90[ASN][1000 genomes]
rs225664	0.90[ASN][1000 genomes]
rs225665	0.90[ASN][1000 genomes]
rs225666	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs225667	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs225668	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs225670	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs225671	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs225672	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs225673	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs225674	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225675	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225676	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs225677	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs225678	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs225679	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225680	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225682	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225683	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225684	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225685	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225686	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225687	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225688	0.85[EUR][1000 genomes]
rs225689	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs225690	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225692	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225693	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225695	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225696	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225697	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225698	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225700	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225701	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225702	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs225704	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225705	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225706	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225707	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225708	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225709	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs225710	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs225728	0.91[ASN][1000 genomes]
rs56185739	0.90[ASN][1000 genomes]
rs62430473	0.83[ASN][1000 genomes]
rs62430506	0.85[ASN][1000 genomes]
rs628311	0.85[ASN][1000 genomes]
rs639658	0.85[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	nsv886732	chr6:142290338-142536049	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv830824	chr6:142361107-142544929	Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142489000-142543200	Weak transcription	Small Intestine	intestine
2	chr6:142496600-142546800	Weak transcription	NHLF	lung
3	chr6:142515400-142541800	Weak transcription	Psoas Muscle	Psoas
4	chr6:142517200-142535400	Weak transcription	Colon Smooth Muscle	Colon
5	chr6:142519600-142535200	Strong transcription	Primary T helper cells PMA-I stimulated	--
6	chr6:142519600-142541800	Strong transcription	HSMM	muscle
7	chr6:142521600-142542600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr6:142523000-142543000	Weak transcription	Stomach Mucosa	stomach
9	chr6:142526000-142535800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr6:142527400-142535800	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr6:142528400-142535200	ZNF genes & repeats	Fetal Lung	lung
12	chr6:142531000-142535200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr6:142531000-142535400	Strong transcription	Primary T cells from cord blood	blood
14	chr6:142531000-142535800	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr6:142531000-142536400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr6:142531000-142537200	Strong transcription	Liver	Liver
17	chr6:142531200-142535200	ZNF genes & repeats	Primary B cells from peripheral blood	blood
18	chr6:142531200-142535200	Strong transcription	Rectal Mucosa Donor 31	rectum
19	chr6:142531200-142536000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr6:142531400-142535200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr6:142531400-142535800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
22	chr6:142531400-142537200	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr6:142531600-142535200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr6:142531800-142535400	ZNF genes & repeats	Fetal Intestine Large	intestine
25	chr6:142531800-142535600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr6:142532200-142535200	Strong transcription	Placenta	Placenta
27	chr6:142532400-142543000	Weak transcription	Fetal Brain Male	brain
28	chr6:142532800-142535600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr6:142532800-142535600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr6:142532800-142536000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:142532800-142536000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr6:142533000-142535200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
33	chr6:142533000-142535200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
34	chr6:142533000-142535200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
35	chr6:142533000-142535200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
36	chr6:142533000-142535200	ZNF genes & repeats	Dnd41	blood
37	chr6:142533000-142535200	Strong transcription	NHDF-Ad	bronchial
38	chr6:142533000-142535800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr6:142533000-142535800	ZNF genes & repeats	Brain Germinal Matrix	brain
40	chr6:142533000-142535800	Strong transcription	A549	lung
41	chr6:142533000-142535800	Strong transcription	HSMMtube	muscle
42	chr6:142533000-142535800	Strong transcription	Osteobl	bone
43	chr6:142533000-142536000	Strong transcription	Adipose Nuclei	Adipose
44	chr6:142533000-142536000	Strong transcription	Stomach Smooth Muscle	stomach
45	chr6:142533000-142536200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr6:142533200-142535200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
47	chr6:142533200-142535200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr6:142533200-142535200	ZNF genes & repeats	GM12878-XiMat	blood
49	chr6:142533200-142535800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr6:142533200-142543200	Weak transcription	HMEC	breast

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