Variant report

Variant	rs2076890
Chromosome Location	chr6:25420744-25420745
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12153885	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12195837	0.96[ASN][1000 genomes]
rs12200019	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12206709	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1304166	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];0.83[TSI][hapmap];0.92[ASN][1000 genomes]
rs1876372	0.88[ASN][1000 genomes]
rs1876373	0.88[ASN][1000 genomes]
rs6905021	0.81[ASN][1000 genomes]
rs72831248	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72831254	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7449710	0.88[ASN][1000 genomes]
rs7760659	0.96[ASN][1000 genomes]
rs9461171	0.88[ASN][1000 genomes]

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	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	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2076890	PRL	cis	cerebellum	SCAN
rs2076890	HIST1H2BC	cis	parietal	SCAN
rs2076890	ZNF184	cis	cerebellum	SCAN
rs2076890	HIST1H2AK	cis	parietal	SCAN
rs2076890	HIST1H1T	cis	parietal	SCAN
rs2076890	HIST1H2AE	cis	lymphoblastoid	seeQTL
rs2076890	C6orf62	cis	cerebellum	SCAN
rs2076890	HIST1H2AD	cis	lymphoblastoid	seeQTL

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25411000-25451800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr6:25414600-25423600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:25415000-25446200	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr6:25415200-25431800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr6:25415600-25421000	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr6:25415600-25422400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr6:25415600-25424000	Weak transcription	Thymus	Thymus
8	chr6:25416200-25441000	Weak transcription	Fetal Thymus	thymus
9	chr6:25416200-25447800	Weak transcription	Pancreas	Pancrea
10	chr6:25416600-25427600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:25416600-25447800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr6:25417600-25431800	Weak transcription	Duodenum Mucosa	Duodenum
13	chr6:25418000-25421200	Weak transcription	Liver	Liver
14	chr6:25418000-25429200	Weak transcription	Aorta	Aorta
15	chr6:25418400-25420800	Weak transcription	Brain Substantia Nigra	brain
16	chr6:25418400-25422000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr6:25418600-25426200	Weak transcription	Gastric	stomach
18	chr6:25418800-25421600	Weak transcription	Adipose Nuclei	Adipose
19	chr6:25418800-25462600	Weak transcription	Ovary	ovary
20	chr6:25419000-25420800	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr6:25419400-25421000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
22	chr6:25419400-25421400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
23	chr6:25419400-25430600	Weak transcription	Left Ventricle	heart
24	chr6:25419600-25420800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
25	chr6:25419600-25421400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
26	chr6:25419800-25420800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr6:25419800-25421400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr6:25419800-25429000	Weak transcription	Small Intestine	intestine
29	chr6:25420000-25421000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
30	chr6:25420000-25421400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr6:25420200-25420800	ZNF genes & repeats	Primary B cells from cord blood	blood
32	chr6:25420200-25420800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr6:25420200-25420800	ZNF genes & repeats	Fetal Intestine Small	intestine
34	chr6:25420200-25421400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr6:25420200-25421400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr6:25420200-25421600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr6:25420400-25420800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr6:25420400-25421000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr6:25420400-25421000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr6:25420400-25421000	Strong transcription	Primary T cells from cord blood	blood
41	chr6:25420400-25421000	Strong transcription	Fetal Lung	lung
42	chr6:25420400-25421400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr6:25420400-25421400	Strong transcription	Fetal Intestine Large	intestine
44	chr6:25420400-25423600	Weak transcription	Right Atrium	heart
45	chr6:25420600-25420800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr6:25420600-25422400	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr6:25420600-25423600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr6:25420600-25423800	Weak transcription	Primary hematopoietic stem cells	blood
49	chr6:25420600-25425400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr6:25420600-25426200	Weak transcription	Pancreatic Islets	Pancreatic Islet

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