Variant report

Variant	rs11856411
Chromosome Location	chr15:57364550-57364551
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 104 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10467927	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.80[EUR][1000 genomes]
rs10467928	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs10467929	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs10851612	0.87[CHB][hapmap]
rs11071303	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11071308	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs11853810	0.86[JPT][hapmap]
rs11856210	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs12101455	0.80[EUR][1000 genomes]
rs13379847	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap]
rs1430820	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1430822	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1657922	0.83[CHB][hapmap]
rs16977153	0.86[CEU][hapmap];0.96[CHB][hapmap];0.90[JPT][hapmap]
rs16977222	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16977243	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16977270	0.86[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap]
rs16977278	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs17415731	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2169467	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2278613	0.87[CHB][hapmap]
rs2414493	0.92[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2439918	0.85[AFR][1000 genomes]
rs2464429	0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs2464430	0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs2464431	0.81[AFR][1000 genomes]
rs2470079	0.93[YRI][hapmap]
rs2470082	0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs2593211	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs2593249	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs2593252	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2615227	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs2703576	0.93[YRI][hapmap];0.83[AFR][1000 genomes]
rs2703614	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2733177	0.85[AFR][1000 genomes]
rs2733185	0.84[AFR][1000 genomes]
rs2733188	0.93[YRI][hapmap]
rs2733333	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2733334	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs28360967	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28372003	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28422021	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28505122	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28533433	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28541606	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28612876	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28648577	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28649108	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28654848	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28677775	0.84[EUR][1000 genomes]
rs28712697	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28756149	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28814080	0.82[EUR][1000 genomes]
rs2920265	0.81[AFR][1000 genomes]
rs2920267	0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs2951895	0.83[AFR][1000 genomes]
rs2951899	0.92[YRI][hapmap]
rs2951903	0.93[YRI][hapmap];0.88[AFR][1000 genomes]
rs2951904	0.92[YRI][hapmap];0.86[AFR][1000 genomes]
rs2962991	0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs2962992	0.93[YRI][hapmap];0.85[AFR][1000 genomes]
rs3803453	0.85[JPT][hapmap]
rs4774245	0.86[CEU][hapmap];0.96[CHB][hapmap];0.90[JPT][hapmap]
rs58479554	0.80[EUR][1000 genomes]
rs6493900	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6493902	0.92[YRI][hapmap]
rs67077316	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7162194	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7163267	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7164655	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[YRI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7169053	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7169508	0.81[EUR][1000 genomes]
rs7171073	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7171304	1.00[CEU][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7173748	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs7175191	0.87[CHB][hapmap]
rs7175436	0.85[YRI][hapmap]
rs7176873	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7178833	1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7180558	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs720290	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap]
rs8023343	0.86[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs8023736	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8023816	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8026702	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs8031516	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8031640	1.00[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8032615	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8033010	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8034066	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8034502	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs8035485	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs8035916	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs8037956	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs8039176	0.86[CHB][hapmap]
rs8039899	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8040708	0.85[EUR][1000 genomes]
rs9302200	1.00[CEU][hapmap];0.83[CHB][hapmap];0.80[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9806170	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9806199	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs997683	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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
3	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11856411	TCF12	Cis_1M	lymphoblastoid	RTeQTL
rs11856411	LOC283663	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57324600-57398600	Weak transcription	Fetal Muscle Leg	muscle
2	chr15:57336600-57371800	Weak transcription	K562	blood
3	chr15:57340200-57372600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr15:57346000-57374400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr15:57347000-57373400	Weak transcription	Fetal Intestine Small	intestine
6	chr15:57347600-57373000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr15:57347600-57373200	Weak transcription	Fetal Intestine Large	intestine
8	chr15:57349800-57366600	Weak transcription	Psoas Muscle	Psoas
9	chr15:57350400-57372400	Weak transcription	Fetal Lung	lung
10	chr15:57350400-57373400	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr15:57350400-57374000	Weak transcription	Ovary	ovary
12	chr15:57351800-57371000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr15:57353400-57371000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr15:57353800-57364800	Weak transcription	HSMM	muscle
15	chr15:57353800-57373800	Weak transcription	Left Ventricle	heart
16	chr15:57353800-57406400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr15:57354200-57384600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr15:57354600-57371600	Weak transcription	NH-A	brain
19	chr15:57355000-57374000	Weak transcription	Osteobl	bone
20	chr15:57355400-57365000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr15:57356000-57393400	Weak transcription	Thymus	Thymus
22	chr15:57356400-57370800	Weak transcription	Primary hematopoietic stem cells	blood
23	chr15:57356400-57371000	Weak transcription	Dnd41	blood
24	chr15:57356400-57371800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr15:57356400-57373800	Weak transcription	Fetal Muscle Trunk	muscle
26	chr15:57356600-57364800	Weak transcription	Fetal Kidney	kidney
27	chr15:57356600-57372000	Weak transcription	Primary B cells from cord blood	blood
28	chr15:57356800-57371200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr15:57357600-57366600	Weak transcription	Primary B cells from peripheral blood	blood
30	chr15:57357600-57371600	Weak transcription	HUVEC	blood vessel
31	chr15:57360200-57371800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr15:57360400-57364800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr15:57360400-57372400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr15:57360600-57371600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr15:57361400-57365800	Enhancers	Brain Anterior Caudate	brain
36	chr15:57361600-57365000	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr15:57361600-57365600	Enhancers	Brain Hippocampus Middle	brain
38	chr15:57361800-57365400	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr15:57362000-57365000	Weak transcription	Primary T cells from cord blood	blood
40	chr15:57362000-57366200	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr15:57362200-57364600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr15:57362200-57364600	Weak transcription	HMEC	breast
43	chr15:57362200-57364600	Weak transcription	NHEK	skin
44	chr15:57362200-57365000	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr15:57362400-57365000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr15:57362400-57371200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr15:57362600-57364800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr15:57362800-57365200	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr15:57362800-57371000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr15:57362800-57384200	Weak transcription	HepG2	liver

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