Variant report

Variant	rs1963831
Chromosome Location	chr15:57208145-57208146
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57207306..57209100-chr15:57209137..57210700,2	K562	blood:

Variant related genes	Relation type
ENSG00000137871	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1015967	0.84[CEU][hapmap];0.86[JPT][hapmap]
rs10438332	0.84[CEU][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes]
rs11632502	0.84[CEU][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes]
rs11632526	0.82[AMR][1000 genomes]
rs11636655	0.84[CEU][hapmap];0.82[CHB][hapmap]
rs11856338	0.90[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.93[JPT][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12437976	0.95[CEU][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12440219	0.85[CEU][hapmap];0.94[EUR][1000 genomes]
rs12591367	0.84[CEU][hapmap];0.86[JPT][hapmap]
rs12595644	0.82[AMR][1000 genomes]
rs12902058	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12906025	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1346880	0.86[JPT][hapmap]
rs1625176	0.84[CEU][hapmap];0.86[JPT][hapmap];0.80[TSI][hapmap]
rs1628974	0.82[AMR][1000 genomes]
rs1631079	0.84[CEU][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.80[TSI][hapmap];0.82[AMR][1000 genomes]
rs1642925	0.85[AMR][1000 genomes]
rs1642927	0.84[CEU][hapmap]
rs1642928	0.82[AMR][1000 genomes]
rs1642936	0.84[CEU][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes]
rs1642940	0.86[JPT][hapmap];0.80[AMR][1000 genomes]
rs1652732	0.84[CEU][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes]
rs1652737	0.83[AMR][1000 genomes]
rs1652738	0.84[CEU][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.80[TSI][hapmap]
rs1652739	0.84[CEU][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.80[TSI][hapmap]
rs1652740	0.84[CEU][hapmap];0.86[JPT][hapmap]
rs1652741	0.84[CEU][hapmap];0.86[JPT][hapmap]
rs1657926	0.84[CEU][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs169893	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17239222	0.84[CEU][hapmap];0.82[CHB][hapmap]
rs1820996	0.82[CHB][hapmap]
rs190039	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs1968399	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1975092	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2111890	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2111892	0.80[AMR][1000 genomes]
rs2116067	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2116068	0.85[EUR][1000 genomes]
rs2126402	0.84[CEU][hapmap];0.82[CHB][hapmap]
rs213148	0.85[AMR][1000 genomes]
rs213152	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs213155	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs213160	0.84[CEU][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs213163	0.84[CEU][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs213166	0.84[CEU][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs213168	0.84[CEU][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2163370	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2169468	0.84[CEU][hapmap];0.82[CHB][hapmap]
rs2252289	0.82[CHB][hapmap];0.80[TSI][hapmap]
rs2435905	0.86[JPT][hapmap];0.80[TSI][hapmap]
rs2439921	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2464427	0.82[CHB][hapmap]
rs2464428	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs2470080	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2470081	0.82[CHB][hapmap];0.86[JPT][hapmap];0.80[TSI][hapmap]
rs2470083	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2470084	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2543675	0.95[CEU][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs2566840	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2566844	0.84[CEU][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.80[TSI][hapmap]
rs2566846	0.82[AMR][1000 genomes]
rs2566856	0.80[TSI][hapmap]
rs2576928	0.81[MKK][hapmap]
rs2585076	0.89[CEU][hapmap];0.86[JPT][hapmap];0.80[TSI][hapmap]
rs2585116	0.84[CEU][hapmap];0.85[JPT][hapmap]
rs2703588	0.82[CHB][hapmap]
rs2733187	0.82[CHB][hapmap];0.89[GIH][hapmap];0.80[TSI][hapmap]
rs28637136	0.89[ASN][1000 genomes]
rs2920270	0.84[CEU][hapmap]
rs2920272	0.86[JPT][hapmap]
rs2951900	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2951902	0.82[CHB][hapmap]
rs2957573	0.86[JPT][hapmap]
rs2957576	0.89[GIH][hapmap];0.86[JPT][hapmap];0.80[TSI][hapmap]
rs2957578	0.82[CHB][hapmap];0.89[GIH][hapmap];0.80[TSI][hapmap]
rs2957592	0.84[CEU][hapmap];0.82[CHB][hapmap]
rs2962994	0.86[JPT][hapmap]
rs2962995	0.84[CEU][hapmap];0.81[CHB][hapmap]
rs34373044	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4581646	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4774246	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4774247	0.90[ASN][1000 genomes]
rs4774900	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7162730	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7164742	0.90[CEU][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs7168945	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7183392	0.86[JPT][hapmap]
rs72749491	0.82[AMR][1000 genomes]
rs7359192	0.84[CEU][hapmap];0.86[JPT][hapmap]
rs8029445	0.84[CEU][hapmap];0.86[JPT][hapmap]
rs8031788	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9806712	0.88[CEU][hapmap];0.85[JPT][hapmap]

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	esv3422474	chr15:56867190-57244330	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv833020	chr15:57055947-57216068	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv457162	chr15:57083006-57225766	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv569577	chr15:57083006-57225766	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv1042486	chr15:57094598-57505992	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv542393	chr15:57115116-57341363	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1963831	TCF12	cis	parietal	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57182000-57209200	Weak transcription	Fetal Stomach	stomach
2	chr15:57194400-57208600	Weak transcription	Left Ventricle	heart
3	chr15:57199000-57209000	Weak transcription	Brain Germinal Matrix	brain
4	chr15:57199200-57209000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:57199400-57209200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr15:57199600-57209000	Weak transcription	Brain Hippocampus Middle	brain
7	chr15:57199600-57209200	Weak transcription	Psoas Muscle	Psoas
8	chr15:57200000-57209000	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr15:57200000-57209000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr15:57200200-57209000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr15:57200200-57209000	Weak transcription	Liver	Liver
12	chr15:57200200-57209200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr15:57200200-57209200	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr15:57200200-57209200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr15:57200400-57209000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr15:57200400-57209000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr15:57200400-57209200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr15:57202600-57209600	Weak transcription	NH-A	brain
19	chr15:57203000-57209000	Weak transcription	Brain Angular Gyrus	brain
20	chr15:57203200-57208200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr15:57203400-57208800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr15:57203400-57209000	Weak transcription	Brain Substantia Nigra	brain
23	chr15:57203400-57209200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr15:57204600-57208400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr15:57204800-57208800	Weak transcription	Thymus	Thymus
26	chr15:57205000-57208600	Weak transcription	Fetal Thymus	thymus
27	chr15:57205600-57209000	Weak transcription	Brain Anterior Caudate	brain
28	chr15:57206000-57208800	Weak transcription	Adipose Nuclei	Adipose
29	chr15:57206000-57209000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr15:57206000-57209800	Weak transcription	HSMM	muscle
31	chr15:57206200-57209000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr15:57206200-57209000	Weak transcription	Fetal Heart	heart
33	chr15:57206200-57209000	Weak transcription	NHDF-Ad	bronchial
34	chr15:57206200-57209200	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr15:57206200-57209200	Weak transcription	HSMMtube	muscle
36	chr15:57206200-57209400	Weak transcription	Dnd41	blood
37	chr15:57206200-57209600	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr15:57206400-57208400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr15:57206400-57209000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr15:57206400-57209000	Weak transcription	HUVEC	blood vessel
41	chr15:57206400-57209200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr15:57206400-57209200	Weak transcription	Osteobl	bone
43	chr15:57206400-57209600	Weak transcription	NHLF	lung
44	chr15:57206800-57209200	Weak transcription	Fetal Kidney	kidney
45	chr15:57207000-57208600	Weak transcription	Pancreas	Pancrea
46	chr15:57207000-57209000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr15:57207000-57209200	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr15:57207000-57209200	Weak transcription	Fetal Intestine Large	intestine
49	chr15:57207000-57209800	Weak transcription	Aorta	Aorta
50	chr15:57207200-57208800	Strong transcription	Fetal Muscle Leg	muscle

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