Variant report

Variant	rs9461170
Chromosome Location	chr6:25436325-25436326
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1028886	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10498725	0.84[GIH][hapmap];1.00[JPT][hapmap]
rs1876372	0.82[JPT][hapmap]
rs1876373	0.82[JPT][hapmap]
rs7761140	0.87[AFR][1000 genomes]
rs9467515	0.83[MKK][hapmap]
rs9467516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467517	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv830612	chr6:25342408-25509758	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv1850810	chr6:25405576-25462543	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs9461170	HIST1H2BM	cis	cerebellum	SCAN
rs9461170	ZNF184	cis	cerebellum	SCAN
rs9461170	HIST1H2AE	cis	parietal	SCAN
rs9461170	HIST1H1T	cis	parietal	SCAN
rs9461170	HIST1H4H	cis	cerebellum	SCAN
rs9461170	ZSCAN12	cis	parietal	SCAN
rs9461170	HIST1H3J	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25411000-25451800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr6:25415000-25446200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr6:25416200-25441000	Weak transcription	Fetal Thymus	thymus
4	chr6:25416200-25447800	Weak transcription	Pancreas	Pancrea
5	chr6:25416600-25447800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:25418800-25462600	Weak transcription	Ovary	ovary
7	chr6:25420800-25436600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:25420800-25441800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr6:25420800-25445400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:25421000-25438600	Weak transcription	Primary B cells from cord blood	blood
11	chr6:25421000-25440400	Weak transcription	Primary T cells from cord blood	blood
12	chr6:25421400-25436400	Weak transcription	Fetal Intestine Large	intestine
13	chr6:25421400-25442200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:25421400-25446200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:25421600-25446200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:25423200-25439800	Weak transcription	NHEK	skin
17	chr6:25427000-25444400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr6:25429600-25436800	Weak transcription	Aorta	Aorta
19	chr6:25432400-25445800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr6:25432400-25447800	Weak transcription	Gastric	stomach
21	chr6:25432600-25445400	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr6:25432800-25436600	Weak transcription	Duodenum Mucosa	Duodenum
23	chr6:25433000-25442400	Weak transcription	Fetal Lung	lung
24	chr6:25433400-25438800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr6:25433400-25439400	Weak transcription	Thymus	Thymus
26	chr6:25433400-25472600	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr6:25433600-25442600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr6:25433800-25437000	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr6:25434000-25446200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr6:25434200-25450200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:25434400-25440400	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr6:25434800-25437000	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr6:25435200-25437000	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr6:25435600-25436800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr6:25435600-25437400	Strong transcription	Fetal Intestine Small	intestine
36	chr6:25435800-25438400	Weak transcription	Esophagus	oesophagus
37	chr6:25435800-25447800	Weak transcription	Lung	lung
38	chr6:25436000-25436800	Enhancers	Monocytes-CD14+_RO01746	blood
39	chr6:25436000-25442200	Weak transcription	Primary hematopoietic stem cells	blood
40	chr6:25436000-25443000	Weak transcription	Primary B cells from peripheral blood	blood
41	chr6:25436000-25445400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr6:25436200-25441000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr6:25436200-25441600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr6:25436200-25481400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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