Variant report

Variant	rs9376478
Chromosome Location	chr6:140204777-140204778
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:140199686..140202479-chr6:140203984..140206544,2	K562	blood:
2	chr6:140202746..140205528-chr6:140208165..140210292,2	K562	blood:
3	chr6:139692335..139698075-chr6:140197375..140205470,17	MCF-7	breast:
4	chr6:140202515..140205528-chr6:140208165..140211710,3	K562	blood:

Variant related genes	Relation type
ENSG00000164442	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs2223966	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs581559	0.94[ASN][1000 genomes]
rs590585	0.84[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs590587	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs592755	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs606159	0.94[ASN][1000 genomes]
rs608122	0.94[ASN][1000 genomes]
rs613274	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs618471	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs627705	0.92[ASN][1000 genomes]
rs629778	0.96[ASN][1000 genomes]
rs633026	0.94[ASN][1000 genomes]
rs654917	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6904492	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7744208	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs7760148	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs9376477	0.85[JPT][hapmap]
rs9399297	0.80[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869066	chr6:139777114-140639695	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv830820	chr6:140059279-140255292	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
3	nsv1017015	chr6:140084137-140300565	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1019407	chr6:140087307-140304334	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1016532	chr6:140174639-141029988	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140201000-140206400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr6:140201800-140205000	Enhancers	Pancreatic Islets	Pancreatic Islet
3	chr6:140201800-140206400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:140202000-140209000	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr6:140202000-140209600	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr6:140202200-140205000	Enhancers	H1 Cell Line	embryonic stem cell
7	chr6:140202200-140206400	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr6:140202400-140205000	Enhancers	Brain Anterior Caudate	brain
9	chr6:140202400-140205200	Enhancers	Brain Substantia Nigra	brain
10	chr6:140202400-140205400	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr6:140202400-140205600	Enhancers	Fetal Heart	heart
12	chr6:140202400-140205600	Enhancers	HSMM	muscle
13	chr6:140202400-140206000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr6:140202400-140206400	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr6:140202400-140211800	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr6:140202600-140205200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr6:140202600-140205800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr6:140202600-140206400	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr6:140203000-140204800	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr6:140203000-140204800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr6:140203000-140204800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr6:140203000-140204800	Enhancers	Duodenum Mucosa	Duodenum
23	chr6:140203000-140204800	Enhancers	Fetal Muscle Leg	muscle
24	chr6:140203000-140204800	Enhancers	Ovary	ovary
25	chr6:140203000-140204800	Enhancers	Psoas Muscle	Psoas
26	chr6:140203000-140204800	Enhancers	K562	blood
27	chr6:140203000-140205000	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr6:140203000-140205000	Enhancers	Rectal Smooth Muscle	rectum
29	chr6:140203000-140205000	Enhancers	HSMMtube	muscle
30	chr6:140203000-140205000	Enhancers	HUVEC	blood vessel
31	chr6:140203000-140205200	Enhancers	Colon Smooth Muscle	Colon
32	chr6:140203000-140205400	Enhancers	NHDF-Ad	bronchial
33	chr6:140203000-140205800	Enhancers	Primary B cells from peripheral blood	blood
34	chr6:140203000-140207400	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr6:140203200-140204800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr6:140203200-140204800	Enhancers	Aorta	Aorta
37	chr6:140203200-140204800	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr6:140203200-140204800	Enhancers	Fetal Intestine Small	intestine
39	chr6:140203200-140204800	Enhancers	Placenta	Placenta
40	chr6:140203200-140204800	Enhancers	Fetal Stomach	stomach
41	chr6:140203200-140204800	Enhancers	Rectal Mucosa Donor 29	rectum
42	chr6:140203200-140205000	Enhancers	GM12878-XiMat	blood
43	chr6:140203200-140205200	Enhancers	Brain Hippocampus Middle	brain
44	chr6:140203200-140205200	Enhancers	Hela-S3	cervix
45	chr6:140203200-140207000	Enhancers	Primary B cells from cord blood	blood
46	chr6:140203200-140209000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr6:140203400-140204800	Enhancers	Brain Angular Gyrus	brain
48	chr6:140203400-140207000	Weak transcription	Spleen	Spleen
49	chr6:140203400-140212600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr6:140203600-140204800	Enhancers	HMEC	breast

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