Variant report

Variant	rs2703614
Chromosome Location	chr15:57459120-57459121
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	chr15:57455822..57459660-chr15:57459793..57463259,4	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	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10467928	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10467929	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11071308	0.83[CHB][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11853810	0.91[JPT][hapmap]
rs11856210	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs11856411	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12101455	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12591430	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13379847	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1430820	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1430822	0.84[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs16977243	0.85[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16977270	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16977278	0.83[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs16977374	0.82[JPT][hapmap]
rs17415731	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1841695	0.84[ASN][1000 genomes]
rs1841697	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2169467	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2414493	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2593211	0.82[CHB][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2593249	0.83[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2593250	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2593252	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2615227	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs2703593	0.81[TSI][hapmap]
rs2703595	0.81[TSI][hapmap]
rs2733323	0.82[JPT][hapmap]
rs2733333	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2733334	0.83[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes]
rs28372003	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28712697	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28781690	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3803453	0.90[GIH][hapmap];0.91[JPT][hapmap]
rs58479554	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6493900	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs67077316	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7162194	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs7163267	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7164298	0.83[CHB][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.83[TSI][hapmap]
rs7169508	0.87[AMR][1000 genomes];0.94[EUR][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];0.81[EUR][1000 genomes]
rs7176873	0.91[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap]
rs7178833	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.80[MEX][hapmap]
rs7180558	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs720290	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs8023736	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8024901	0.91[JPT][hapmap]
rs8026702	0.83[CHB][hapmap];0.91[JPT][hapmap];0.94[TSI][hapmap]
rs8031640	0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs8032615	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs8034066	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs8034502	0.83[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8034744	0.89[TSI][hapmap]
rs8034843	0.95[GIH][hapmap];0.85[JPT][hapmap]
rs8035916	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8037956	0.81[CHB][hapmap];0.87[JPT][hapmap]
rs8039176	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs8039899	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9302200	0.85[CEU][hapmap];0.83[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];0.94[TSI][hapmap]
rs9672676	0.89[TSI][hapmap]
rs9806170	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9806199	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][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
rs2703614	TCF12	Cis_1M	lymphoblastoid	RTeQTL
rs2703614	LOC283663	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57439000-57463400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr15:57439400-57491600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr15:57444400-57459200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr15:57444400-57485600	Weak transcription	Placenta	Placenta
5	chr15:57444400-57507400	Weak transcription	K562	blood
6	chr15:57444600-57459600	Weak transcription	Liver	Liver
7	chr15:57444600-57490200	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr15:57444800-57484200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr15:57444800-57484200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr15:57445000-57461600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr15:57445200-57466000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr15:57445400-57478400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr15:57445600-57461400	Weak transcription	Primary B cells from peripheral blood	blood
14	chr15:57446000-57468400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr15:57446600-57459600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:57447000-57484600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr15:57447800-57466000	Weak transcription	Pancreas	Pancrea
18	chr15:57448000-57465600	Weak transcription	Right Ventricle	heart
19	chr15:57448000-57483800	Weak transcription	Lung	lung
20	chr15:57448800-57460200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr15:57448800-57463400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr15:57450800-57459400	Weak transcription	Fetal Muscle Trunk	muscle
23	chr15:57450800-57469000	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr15:57450800-57491000	Weak transcription	Left Ventricle	heart
25	chr15:57451000-57464400	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr15:57451000-57477400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr15:57451000-57487800	Weak transcription	Psoas Muscle	Psoas
28	chr15:57451000-57490800	Weak transcription	NHEK	skin
29	chr15:57451200-57459200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr15:57451200-57463600	Weak transcription	Hela-S3	cervix
31	chr15:57451200-57470200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr15:57451200-57475000	Weak transcription	Colon Smooth Muscle	Colon
33	chr15:57451200-57475400	Weak transcription	Adipose Nuclei	Adipose
34	chr15:57451200-57478600	Weak transcription	HMEC	breast
35	chr15:57451200-57484200	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr15:57451200-57484200	Weak transcription	Esophagus	oesophagus
37	chr15:57451200-57490400	Weak transcription	Ovary	ovary
38	chr15:57451400-57463200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr15:57451400-57463600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr15:57451600-57491200	Weak transcription	Rectal Smooth Muscle	rectum
41	chr15:57451800-57478400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr15:57452200-57459200	Weak transcription	Fetal Stomach	stomach
43	chr15:57452200-57459200	Weak transcription	HSMMtube	muscle
44	chr15:57452200-57481600	Weak transcription	Fetal Heart	heart
45	chr15:57452400-57465000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr15:57452400-57475400	Weak transcription	Fetal Lung	lung
47	chr15:57452400-57490400	Weak transcription	Fetal Brain Female	brain
48	chr15:57452600-57460400	Weak transcription	Brain Substantia Nigra	brain
49	chr15:57452800-57460800	Weak transcription	Brain Hippocampus Middle	brain
50	chr15:57452800-57470800	Weak transcription	Brain Anterior Caudate	brain

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