Variant report

Variant	rs11196825
Chromosome Location	chr10:116405990-116405991
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:116404550..116406229-chr4:106628340..106629882,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138785	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10444096	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10444097	0.89[ASN][1000 genomes]
rs10787539	0.92[JPT][hapmap]
rs10787540	0.91[JPT][hapmap]
rs11196798	0.91[JPT][hapmap]
rs11196802	0.91[JPT][hapmap]
rs11196804	0.85[ASN][1000 genomes]
rs11196806	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11196810	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11196813	0.89[ASN][1000 genomes]
rs11196814	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11196826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11196844	0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs11196845	0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs11196853	0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs11196854	0.91[JPT][hapmap];1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11196856	0.92[ASN][1000 genomes]
rs11196858	0.92[ASN][1000 genomes]
rs11196859	0.91[ASN][1000 genomes]
rs11196861	0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs12146316	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12359503	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12360417	0.87[ASN][1000 genomes]
rs12763337	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12768716	0.91[JPT][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12772864	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17719647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34811081	0.89[ASN][1000 genomes]
rs4237504	0.89[ASN][1000 genomes]
rs4751620	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4752039	0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4752040	0.87[ASN][1000 genomes]
rs4752044	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4752047	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4752071	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4752089	0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs7080854	0.91[JPT][hapmap]
rs7094673	0.91[JPT][hapmap]
rs7907371	0.91[ASN][1000 genomes]
rs955634	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037308	chr10:116141946-116519765	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv540780	chr10:116141946-116519765	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv949138	chr10:116311531-116874477	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1038050	chr10:116315109-116895719	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv533027	chr10:116344641-116856352	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	esv3435429	chr10:116394152-117006347	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11196825	ADRB1,NHLRC2	cis	putamen	BrainEAC

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116394400-116422600	Weak transcription	Fetal Intestine Small	intestine
2	chr10:116395800-116408400	Weak transcription	Psoas Muscle	Psoas
3	chr10:116396200-116408800	Weak transcription	Esophagus	oesophagus
4	chr10:116397200-116409400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr10:116399200-116410400	Weak transcription	Brain Angular Gyrus	brain
6	chr10:116399600-116408600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr10:116399800-116413800	Weak transcription	Spleen	Spleen
8	chr10:116400000-116406000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr10:116400200-116408600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr10:116402000-116408400	Weak transcription	Right Ventricle	heart
11	chr10:116402800-116407000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr10:116402800-116407000	Weak transcription	HMEC	breast
13	chr10:116403000-116408000	Weak transcription	Stomach Mucosa	stomach
14	chr10:116403200-116407200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr10:116403200-116408000	Weak transcription	Adipose Nuclei	Adipose
16	chr10:116403200-116412200	Weak transcription	Brain Anterior Caudate	brain
17	chr10:116404400-116407400	Enhancers	A549	lung
18	chr10:116404400-116409400	Weak transcription	Gastric	stomach
19	chr10:116404400-116411000	Enhancers	Fetal Heart	heart
20	chr10:116404600-116406200	Enhancers	Liver	Liver
21	chr10:116404600-116406400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr10:116404600-116411200	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr10:116404800-116406200	Enhancers	Fetal Lung	lung
24	chr10:116404800-116407800	Enhancers	Hela-S3	cervix
25	chr10:116404800-116409600	Enhancers	Muscle Satellite Cultured Cells	--
26	chr10:116404800-116412200	Weak transcription	Lung	lung
27	chr10:116405000-116406400	Enhancers	Pancreatic Islets	Pancreatic Islet
28	chr10:116405000-116406600	Enhancers	HSMM	muscle
29	chr10:116405000-116407400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr10:116405000-116409400	Weak transcription	Pancreas	Pancrea
31	chr10:116405200-116406000	Weak transcription	Brain Cingulate Gyrus	brain
32	chr10:116405200-116406000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr10:116405200-116406200	Weak transcription	Left Ventricle	heart
34	chr10:116405200-116406200	Weak transcription	Right Atrium	heart
35	chr10:116405200-116407000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr10:116405200-116407000	Weak transcription	NHEK	skin
37	chr10:116405200-116413400	Weak transcription	Colonic Mucosa	Colon
38	chr10:116405600-116406200	Flanking Active TSS	HUVEC	blood vessel
39	chr10:116405600-116406600	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr10:116405600-116406600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr10:116405600-116407200	Weak transcription	NHLF	lung
42	chr10:116405800-116406000	Enhancers	NHDF-Ad	bronchial
43	chr10:116405800-116408200	Enhancers	Rectal Mucosa Donor 29	rectum

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