Variant report

Variant	rs7975996
Chromosome Location	chr12:10524923-10524924
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1049172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1049174	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs11053801	0.95[CEU][hapmap]
rs11053802	0.95[CEU][hapmap]
rs12824474	1.00[JPT][hapmap]
rs1351113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1600128	0.91[EUR][1000 genomes]
rs1841957	0.95[CEU][hapmap]
rs1841958	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs1904123	0.91[EUR][1000 genomes]
rs2086098	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs2086099	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2250877	0.89[EUR][1000 genomes]
rs2255336	0.83[MEX][hapmap]
rs2617149	1.00[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs2617150	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2617160	1.00[CEU][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs2617170	0.95[CEU][hapmap]
rs2617171	0.95[CEU][hapmap]
rs2733840	0.82[MEX][hapmap]
rs2733841	0.88[EUR][1000 genomes]
rs2733845	0.82[MEX][hapmap]
rs2733851	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2733852	1.00[CEU][hapmap];0.95[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2734565	0.95[CEU][hapmap];1.00[GIH][hapmap];0.82[EUR][1000 genomes]
rs4764430	0.81[CHD][hapmap]
rs7310643	0.86[CHD][hapmap]
rs7978962	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898757	chr12:10229281-10614641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv832328	chr12:10398071-10620443	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv898759	chr12:10454556-10583365	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv3432683	chr12:10470734-10527581	Genic enhancers Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv898760	chr12:10492982-10564329	Genic enhancers Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv898761	chr12:10496724-10564329	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv1036390	chr12:10496724-10596720	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv557455	chr12:10508975-10560957	Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv898762	chr12:10509383-10564329	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
10	nsv898763	chr12:10514528-10603670	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7975996	PRB3	cis	parietal	SCAN
rs7975996	LRRC23	cis	cerebellum	SCAN
rs7975996	TAS2R9	cis	parietal	SCAN
rs7975996	NCAPD2	cis	cerebellum	SCAN
rs7975996	KLRK1	cis	lymphoblastoid	seeQTL
rs7975996	RP11-277P12.20	cis	Esophagus Mucosa	GTEx
rs7975996	ENO2	cis	parietal	SCAN
rs7975996	CD69	cis	cerebellum	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10518400-10537000	Weak transcription	Left Ventricle	heart
2	chr12:10518600-10525200	Weak transcription	Lung	lung
3	chr12:10518600-10526600	Enhancers	Primary T killer memory cells from peripheral blood	blood
4	chr12:10518800-10527400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr12:10519000-10525200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr12:10519200-10525200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr12:10519200-10525200	Weak transcription	Spleen	Spleen
8	chr12:10519200-10525400	Weak transcription	Aorta	Aorta
9	chr12:10519400-10525000	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr12:10519400-10525000	Weak transcription	Pancreas	Pancrea
11	chr12:10519400-10525200	Weak transcription	Esophagus	oesophagus
12	chr12:10519400-10525200	Weak transcription	Right Atrium	heart
13	chr12:10519600-10525000	Weak transcription	Primary hematopoietic stem cells	blood
14	chr12:10519600-10525000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr12:10519600-10525200	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr12:10519600-10525200	Weak transcription	Colonic Mucosa	Colon
17	chr12:10519600-10525200	Weak transcription	Small Intestine	intestine
18	chr12:10519600-10534800	Weak transcription	Fetal Stomach	stomach
19	chr12:10519600-10547800	Weak transcription	Colon Smooth Muscle	Colon
20	chr12:10520000-10525200	Weak transcription	Fetal Intestine Small	intestine
21	chr12:10520200-10525000	Weak transcription	Fetal Intestine Large	intestine
22	chr12:10520400-10525000	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr12:10520400-10525200	Weak transcription	Primary B cells from peripheral blood	blood
24	chr12:10521200-10531000	Weak transcription	Placenta	Placenta
25	chr12:10521400-10525200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr12:10521400-10525200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr12:10521600-10525000	Weak transcription	Brain Anterior Caudate	brain
28	chr12:10521600-10525200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr12:10521600-10525200	Weak transcription	Brain Angular Gyrus	brain
30	chr12:10521800-10525000	Weak transcription	Adipose Nuclei	Adipose
31	chr12:10521800-10526400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr12:10521800-10534600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr12:10522200-10525600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr12:10522400-10525200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr12:10522400-10530200	Weak transcription	Fetal Thymus	thymus
36	chr12:10522400-10534000	Weak transcription	Thymus	Thymus
37	chr12:10522800-10525000	Weak transcription	Primary T cells from cord blood	blood
38	chr12:10523000-10525000	Weak transcription	Brain Cingulate Gyrus	brain
39	chr12:10523000-10525000	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr12:10523000-10536000	Weak transcription	Ovary	ovary
41	chr12:10523200-10525800	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr12:10523400-10525800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr12:10523400-10525800	Enhancers	HUVEC	blood vessel
44	chr12:10523400-10527400	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr12:10523600-10525000	Weak transcription	Brain Substantia Nigra	brain
46	chr12:10523600-10525600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr12:10523600-10532000	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
48	chr12:10523800-10525200	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr12:10523800-10525400	Enhancers	HMEC	breast
50	chr12:10523800-10525800	Enhancers	Primary B cells from cord blood	blood

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