Variant report

Variant	rs2169467
Chromosome Location	chr15:57414495-57414496
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57411738..57417145-chr15:57421254..57425802,5	K562	blood:

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10467927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10467928	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10467929	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11071308	0.83[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs11853810	0.91[JPT][hapmap]
rs11856210	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs11856411	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12101455	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12591430	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13379847	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1430820	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1430822	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs16977153	0.86[CEU][hapmap];0.96[CHB][hapmap];0.85[JPT][hapmap]
rs16977243	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16977270	0.86[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16977278	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs16977374	0.82[JPT][hapmap]
rs17415731	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1841697	0.84[EUR][1000 genomes]
rs2414493	0.83[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap]
rs2593211	0.82[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes]
rs2593249	0.83[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes]
rs2593250	0.86[EUR][1000 genomes]
rs2593252	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2615227	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs2703614	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2733323	0.82[JPT][hapmap]
rs2733333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2733334	0.83[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes]
rs28372003	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28712697	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28781690	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3803453	0.91[JPT][hapmap]
rs4774245	0.86[CEU][hapmap];0.96[CHB][hapmap];0.85[JPT][hapmap]
rs58479554	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6493900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67077316	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7162194	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs7163267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7164298	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs7164655	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs7169508	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7171073	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs7171304	1.00[CEU][hapmap]
rs7173748	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs7176873	0.91[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs7178833	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs7180558	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs720290	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs8023343	0.86[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap]
rs8023736	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8024901	0.91[JPT][hapmap]
rs8026702	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs8031640	1.00[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap]
rs8032615	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap]
rs8034066	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs8034502	0.83[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes]
rs8034843	0.85[JPT][hapmap]
rs8035485	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs8035916	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8037956	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs8039176	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs8039899	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9302200	1.00[CEU][hapmap];0.83[CHB][hapmap]
rs9806170	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9806199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs997683	0.91[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
rs2169467	TCF12	Cis_1M	lymphoblastoid	RTeQTL
rs2169467	LOC283663	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57374800-57414600	Weak transcription	Fetal Kidney	kidney
2	chr15:57382600-57423800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr15:57382800-57419600	Weak transcription	K562	blood
4	chr15:57386400-57426600	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr15:57386600-57424600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr15:57387000-57430000	Weak transcription	Placenta	Placenta
7	chr15:57387200-57425400	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr15:57387600-57442400	Weak transcription	Fetal Intestine Large	intestine
9	chr15:57397800-57416600	Weak transcription	Fetal Stomach	stomach
10	chr15:57398000-57415800	Weak transcription	Fetal Intestine Small	intestine
11	chr15:57399400-57424600	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr15:57399600-57416200	Weak transcription	Primary T cells from cord blood	blood
13	chr15:57402600-57414600	Weak transcription	Primary B cells from cord blood	blood
14	chr15:57403000-57424600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr15:57403800-57425200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr15:57404600-57425000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr15:57404800-57415600	Weak transcription	Thymus	Thymus
18	chr15:57406800-57414600	Weak transcription	Colon Smooth Muscle	Colon
19	chr15:57406800-57416200	Weak transcription	Fetal Muscle Leg	muscle
20	chr15:57406800-57425000	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr15:57406800-57425400	Weak transcription	Pancreas	Pancrea
22	chr15:57406800-57425600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr15:57406800-57425600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr15:57406800-57426400	Weak transcription	Colonic Mucosa	Colon
25	chr15:57406800-57426600	Weak transcription	Psoas Muscle	Psoas
26	chr15:57407600-57425600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr15:57409400-57415600	Enhancers	Brain Hippocampus Middle	brain
28	chr15:57410200-57414800	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr15:57410200-57415200	Enhancers	iPS-20b Cell Line	embryonic stem cell
30	chr15:57410400-57414600	Weak transcription	Rectal Smooth Muscle	rectum
31	chr15:57410400-57425400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr15:57410600-57415400	Enhancers	Brain Cingulate Gyrus	brain
33	chr15:57410600-57415600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr15:57410600-57416400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr15:57410600-57416400	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr15:57410600-57419800	Weak transcription	HepG2	liver
37	chr15:57410600-57421600	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr15:57410600-57424800	Weak transcription	HSMMtube	muscle
39	chr15:57410600-57425000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr15:57410600-57425400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr15:57410600-57426600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr15:57410600-57440800	Weak transcription	Ovary	ovary
43	chr15:57410800-57415000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr15:57410800-57416400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr15:57410800-57425000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr15:57410800-57425000	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr15:57410800-57425600	Weak transcription	HMEC	breast
48	chr15:57411000-57416200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr15:57411000-57428200	Weak transcription	NHLF	lung
50	chr15:57411000-57430400	Weak transcription	NH-A	brain

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