Variant report

Variant	rs11856338
Chromosome Location	chr15:57273239-57273240
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:57265601..57267263-chr15:57271593..57273612,2	K562	blood:
2	chr15:57273239..57275335-chr15:57275612..57277322,2	K562	blood:
3	chr15:57269633..57272065-chr15:57273062..57274627,2	K562	blood:

Extended variants
information (count: 105 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs1015967	0.81[CHB][hapmap];0.93[JPT][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10438332	0.81[CHB][hapmap];0.93[JPT][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11071302	0.81[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs11071307	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs1139006	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11630965	0.96[EUR][1000 genomes]
rs11632502	0.81[CHB][hapmap];0.93[JPT][hapmap];0.91[EUR][1000 genomes]
rs11632526	0.91[EUR][1000 genomes]
rs11636655	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs12148850	0.86[EUR][1000 genomes]
rs12437976	0.95[CEU][hapmap];0.89[TSI][hapmap]
rs12440219	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs12591367	0.81[CHB][hapmap];0.93[JPT][hapmap];0.88[EUR][1000 genomes]
rs12593843	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs12595644	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12902058	0.95[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12906025	1.00[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.95[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1346880	0.81[CHB][hapmap];0.93[JPT][hapmap];0.87[EUR][1000 genomes]
rs1367491	0.87[EUR][1000 genomes]
rs1625176	0.81[CHB][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1628974	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1631079	0.81[CHB][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1642925	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1642927	0.88[EUR][1000 genomes]
rs1642928	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1642929	0.89[EUR][1000 genomes]
rs1642935	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1642936	0.81[CHB][hapmap];0.93[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1642937	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1642940	0.90[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1652732	0.81[CHB][hapmap];0.93[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1652737	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1652738	0.81[CHB][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs1652739	0.81[CHB][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1652740	0.81[CHB][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1652741	0.81[CHB][hapmap];0.93[JPT][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1657926	0.93[JPT][hapmap]
rs17239222	0.90[CHB][hapmap]
rs17415731	0.83[AFR][1000 genomes]
rs17819940	0.93[GIH][hapmap];0.86[JPT][hapmap];0.92[TSI][hapmap]
rs1820996	0.90[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs190039	0.83[EUR][1000 genomes]
rs1963831	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]
rs1968399	0.84[ASN][1000 genomes]
rs2111890	1.00[ASW][hapmap];0.91[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.95[LWK][hapmap];0.95[MKK][hapmap];0.92[TSI][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2126402	0.90[CHB][hapmap]
rs213148	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs213155	0.91[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs213160	0.81[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes]
rs213163	0.93[GIH][hapmap];0.92[JPT][hapmap];0.92[TSI][hapmap]
rs213166	0.81[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes]
rs213168	0.93[JPT][hapmap];0.84[EUR][1000 genomes]
rs2163370	0.91[ASN][1000 genomes]
rs2169468	0.90[CHB][hapmap]
rs2252289	0.90[CHB][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.95[TSI][hapmap]
rs2435905	0.81[CHB][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs2439921	0.82[EUR][1000 genomes]
rs2439925	0.88[EUR][1000 genomes]
rs2464427	0.90[CHB][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.92[TSI][hapmap]
rs2464428	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs2470080	0.90[CHB][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes]
rs2470081	0.90[CHB][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs2470083	0.90[CHB][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes]
rs2470084	0.90[CHB][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes]
rs2543675	0.95[CEU][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs2566840	0.95[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2566844	0.81[CHB][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2566846	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2566856	0.81[GIH][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs2585076	0.82[CEU][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs2585116	0.81[CHB][hapmap];0.92[JPT][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2703588	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs2733187	0.90[CHB][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.95[TSI][hapmap]
rs28637136	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2915176	0.86[EUR][1000 genomes]
rs2920272	0.93[JPT][hapmap];0.87[EUR][1000 genomes]
rs2951900	0.90[CHB][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes]
rs2951902	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs2957573	0.81[CHB][hapmap];0.93[JPT][hapmap];0.87[EUR][1000 genomes]
rs2957576	0.81[CHB][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs2957578	0.90[CHB][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.95[TSI][hapmap]
rs2957592	0.90[CHB][hapmap]
rs2962994	0.81[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes]
rs2962995	0.90[CHB][hapmap]
rs3794617	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs4774245	0.82[YRI][hapmap]
rs4774246	1.00[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.93[LWK][hapmap];0.95[MKK][hapmap];0.92[TSI][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4774247	0.97[ASN][1000 genomes]
rs55886927	0.84[EUR][1000 genomes]
rs7162730	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7164742	0.91[CEU][hapmap];0.90[TSI][hapmap]
rs7168945	0.95[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7183392	0.81[CHB][hapmap];0.93[JPT][hapmap];0.86[EUR][1000 genomes]
rs72749478	0.89[EUR][1000 genomes]
rs72749491	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7359192	0.81[CHB][hapmap];0.93[JPT][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8029445	0.81[CHB][hapmap];0.93[JPT][hapmap];0.88[EUR][1000 genomes]
rs8035485	0.84[YRI][hapmap]
rs9806712	0.81[CEU][hapmap];0.81[CHB][hapmap];0.92[JPT][hapmap];0.91[EUR][1000 genomes];0.82[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	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
2	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
3	nsv904250	chr15:57225766-57294085	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv1052052	chr15:57232111-57344561	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv542394	chr15:57232111-57344561	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv904251	chr15:57241970-57575916	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11856338	TCF12	cis	parietal	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57256800-57277200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr15:57257200-57274600	Weak transcription	Adipose Nuclei	Adipose
3	chr15:57261200-57279000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr15:57261400-57275000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr15:57262200-57280000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr15:57263800-57276000	Weak transcription	Lung	lung
7	chr15:57264800-57275000	Weak transcription	Duodenum Mucosa	Duodenum
8	chr15:57264800-57275200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr15:57265400-57277000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr15:57266200-57274200	Weak transcription	Liver	Liver
11	chr15:57267000-57273400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr15:57267000-57274600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr15:57267400-57274000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr15:57269800-57273800	Enhancers	Brain Hippocampus Middle	brain
15	chr15:57269800-57275200	Weak transcription	Right Ventricle	heart
16	chr15:57269800-57276400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr15:57269800-57304800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr15:57270000-57276800	Weak transcription	HSMMtube	muscle
19	chr15:57270000-57280200	Weak transcription	Fetal Brain Male	brain
20	chr15:57270800-57273600	Enhancers	Muscle Satellite Cultured Cells	--
21	chr15:57271000-57273600	Enhancers	K562	blood
22	chr15:57271000-57273800	Enhancers	Brain Cingulate Gyrus	brain
23	chr15:57271200-57276200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr15:57271400-57275000	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr15:57271400-57276400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr15:57271600-57274400	Enhancers	Brain Anterior Caudate	brain
27	chr15:57271600-57275200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr15:57271600-57275800	Enhancers	Brain Substantia Nigra	brain
29	chr15:57271600-57276600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr15:57271800-57273800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr15:57271800-57275000	Weak transcription	HepG2	liver
32	chr15:57271800-57276600	Weak transcription	NHLF	lung
33	chr15:57272000-57273400	Enhancers	Colon Smooth Muscle	Colon
34	chr15:57272000-57274600	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr15:57272000-57275000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr15:57272000-57275400	Enhancers	A549	lung
37	chr15:57272000-57275800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr15:57272000-57276800	Weak transcription	Hela-S3	cervix
39	chr15:57272200-57273600	Enhancers	Small Intestine	intestine
40	chr15:57272200-57273600	Weak transcription	HUVEC	blood vessel
41	chr15:57272200-57273800	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr15:57272200-57274200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr15:57272200-57274200	Genic enhancers	Fetal Thymus	thymus
44	chr15:57272200-57274400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr15:57272200-57276000	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr15:57272200-57276600	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr15:57272200-57276600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr15:57272200-57280600	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr15:57272200-57282400	Enhancers	Primary T cells from cord blood	blood
50	chr15:57272400-57274200	Enhancers	Fetal Intestine Large	intestine

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