Variant report

Variant	rs2238034
Chromosome Location	chr12:2235628-2235629
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1005618	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1122864	0.92[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1558321	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs1558322	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs2238029	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs2238036	0.83[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[ASN][1000 genomes]
rs2238042	0.88[CEU][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes]
rs2239131	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs2239136	0.94[CEU][hapmap];0.86[GIH][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs2247833	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2283285	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2299660	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs4765898	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.84[MKK][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:35 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948480	chr12:1776217-2284333	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1040370	chr12:2021395-2671017	Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv948400	chr12:2022411-2601363	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv521838	chr12:2060580-2299680	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1035885	chr12:2077660-2310157	Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv541350	chr12:2077660-2310157	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1038722	chr12:2085035-2308205	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv541351	chr12:2085035-2308205	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv826183	chr12:2147469-2257818	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv898603	chr12:2208390-2268143	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv1053798	chr12:2214047-2253488	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv557033	chr12:2215448-2252924	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv1041740	chr12:2218997-2259643	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv557034	chr12:2226045-2251273	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv1052890	chr12:2226045-2251869	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv557035	chr12:2227311-2252924	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
17	nsv468967	chr12:2227311-2268143	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
18	nsv557036	chr12:2227311-2268143	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
19	nsv1041632	chr12:2230012-2257585	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
20	nsv557037	chr12:2230055-2257916	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
21	nsv1036646	chr12:2232157-2257908	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
22	nsv1039310	chr12:2232157-2258394	Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
23	esv2760788	chr12:2232157-2270291	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
24	nsv557038	chr12:2233023-2257495	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
25	nsv1044373	chr12:2233929-2258394	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
26	nsv1049985	chr12:2233929-2260754	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
27	nsv521953	chr12:2235628-2247179	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	n/a	n/a	inside rSNPs	diseases
28	nsv1051298	chr12:2235628-2254677	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
29	nsv557039	chr12:2235628-2257495	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
30	nsv1054901	chr12:2235628-2258394	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
31	nsv1042716	chr12:2235628-2259955	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
32	nsv1045863	chr12:2235628-2260754	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
33	nsv557040	chr12:2235628-2268143	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
34	nsv468968	chr12:2235628-2269588	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
35	nsv557041	chr12:2235628-2269588	Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2238034	WNK1	cis	cerebellum	SCAN
rs2238034	NRIP2	cis	parietal	SCAN
rs2238034	KCNA1	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:2222400-2239000	Weak transcription	Brain Anterior Caudate	brain
2	chr12:2222800-2236000	Weak transcription	Lung	lung
3	chr12:2223200-2250200	Weak transcription	Brain Substantia Nigra	brain
4	chr12:2223600-2238200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:2227800-2235800	Weak transcription	Fetal Kidney	kidney
6	chr12:2228000-2235800	Weak transcription	Brain Angular Gyrus	brain
7	chr12:2229800-2237200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr12:2229800-2245600	Weak transcription	Stomach Mucosa	stomach
9	chr12:2230400-2237800	Weak transcription	NHDF-Ad	bronchial
10	chr12:2231000-2238000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:2231200-2238000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr12:2231600-2240000	Weak transcription	NHLF	lung
13	chr12:2231800-2238000	Weak transcription	Osteobl	bone
14	chr12:2232000-2246800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr12:2232200-2236600	Weak transcription	Fetal Intestine Small	intestine
16	chr12:2232200-2254800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr12:2232400-2245400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr12:2233200-2236800	Enhancers	Fetal Heart	heart
19	chr12:2233600-2235800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr12:2234200-2236400	Enhancers	Right Atrium	heart
21	chr12:2234200-2238000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr12:2234200-2247000	Weak transcription	Spleen	Spleen
23	chr12:2234400-2235800	Genic enhancers	Stomach Smooth Muscle	stomach
24	chr12:2234400-2238000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr12:2234600-2236400	Genic enhancers	Fetal Stomach	stomach
26	chr12:2234800-2236400	Enhancers	Fetal Lung	lung
27	chr12:2235000-2235800	Weak transcription	Aorta	Aorta
28	chr12:2235000-2235800	Enhancers	Right Ventricle	heart
29	chr12:2235000-2236400	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr12:2235000-2239200	Enhancers	Rectal Smooth Muscle	rectum
31	chr12:2235200-2237200	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr12:2235400-2235800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr12:2235400-2236000	Enhancers	Fetal Brain Male	brain
34	chr12:2235400-2236200	Enhancers	Pancreatic Islets	Pancreatic Islet
35	chr12:2235400-2237000	Enhancers	Left Ventricle	heart
36	chr12:2235400-2238000	Enhancers	Colon Smooth Muscle	Colon

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