Variant report

Variant	rs12895620
Chromosome Location	chr14:69863843-69863844
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr14:69863548-69866554	MCF10A-Er-Src	breast:	n/a	n/a
2	MXI1	chr14:69863745-69866480	IMR90	lung:	n/a	n/a
3	POLR2A	chr14:69863800-69866247	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr14:69863699-69866185	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr14:69863778-69866182	GM12878	blood:	n/a	n/a
6	POLR2A	chr14:69863841-69866266	GM12891	blood:	n/a	n/a
7	MYC	chr14:69863494-69863958	MCF10A-Er-Src	breast:	n/a	chr14:69863651-69863660 chr14:69863652-69863661 chr14:69863653-69863660 chr14:69863652-69863662 chr14:69863651-69863662
8	POLR2A	chr14:69863393-69865605	K562	blood:	n/a	n/a
9	MYC	chr14:69863494-69863844	MCF10A-Er-Src	breast:	n/a	chr14:69863651-69863660 chr14:69863652-69863661 chr14:69863653-69863660 chr14:69863652-69863662 chr14:69863651-69863662
10	POLR2A	chr14:69863689-69866550	MCF10A-Er-Src	breast:	n/a	n/a
11	HCFC1	chr14:69863374-69866025	Hela-S3	cervix:	n/a	n/a
12	MXI1	chr14:69863406-69864313	GM12878	blood:	n/a	chr14:69863651-69863660

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:69863611..69866530-chr14:81685832..81688549,2	K562	blood:
2	chr14:69618202..69621032-chr14:69863576..69866501,3	MCF-7	breast:

Variant related genes	Relation type
SLC39A9	TF binding region
ERH	TF binding region
ENSG00000139990	Chromatin interaction
ENSG00000165417	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10083335	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10129186	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10129720	0.85[AMR][1000 genomes]
rs10138313	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10140273	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10142144	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10143593	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10143710	0.81[EUR][1000 genomes]
rs10151691	0.94[ASW][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes]
rs11622711	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11623094	0.82[CEU][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11624577	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12147478	0.82[AMR][1000 genomes]
rs12147967	0.82[AMR][1000 genomes]
rs12878175	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12884348	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12884802	0.91[ASN][1000 genomes]
rs12893282	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1455053	0.81[JPT][hapmap]
rs1466255	0.82[AMR][1000 genomes]
rs1958121	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1965878	0.82[AMR][1000 genomes]
rs2085193	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2124191	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2124192	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs2296722	0.94[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2296724	0.94[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2296725	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2296727	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28401542	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28451089	0.90[AMR][1000 genomes]
rs28470369	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28661733	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28879441	0.81[EUR][1000 genomes]
rs34405286	0.82[AMR][1000 genomes]
rs34450502	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34731892	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34834622	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34840252	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3759770	0.82[CEU][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3759771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4899294	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4899295	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902717	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56137363	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56392460	0.82[AMR][1000 genomes]
rs56953348	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58553067	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67502261	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71423356	0.91[ASN][1000 genomes]
rs7143858	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7145944	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7147362	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7147710	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7150586	0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7159476	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7160248	0.82[AMR][1000 genomes]
rs8010767	0.82[AMR][1000 genomes]
rs8012954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8014890	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8015317	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8015425	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8016781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8020817	0.81[EUR][1000 genomes]
rs959242	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12895620	SLC39A9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:69824200-69864000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr14:69854200-69864000	Weak transcription	Aorta	Aorta
3	chr14:69860800-69864000	Weak transcription	Pancreas	Pancrea
4	chr14:69861400-69864000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr14:69861400-69864000	Weak transcription	Gastric	stomach
6	chr14:69861400-69864000	Weak transcription	Spleen	Spleen
7	chr14:69862000-69864000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr14:69862000-69864000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr14:69862000-69864000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr14:69862000-69864000	Weak transcription	Esophagus	oesophagus
11	chr14:69862000-69864000	Weak transcription	Left Ventricle	heart
12	chr14:69862200-69864000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr14:69862400-69864000	Transcr. at gene 5' and 3'	Hela-S3	cervix
14	chr14:69862400-69864200	Transcr. at gene 5' and 3'	Dnd41	blood
15	chr14:69862600-69864000	Weak transcription	Ovary	ovary
16	chr14:69863000-69864000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr14:69863000-69864000	Enhancers	Fetal Muscle Trunk	muscle
18	chr14:69863000-69864000	Weak transcription	Placenta	Placenta
19	chr14:69863000-69864000	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr14:69863200-69864000	Enhancers	Primary B cells from peripheral blood	blood
21	chr14:69863200-69864000	Weak transcription	Lung	lung
22	chr14:69863200-69864200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr14:69863400-69864000	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr14:69863400-69864000	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr14:69863400-69864000	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr14:69863400-69864000	Enhancers	Small Intestine	intestine
27	chr14:69863400-69864000	Flanking Active TSS	HepG2	liver
28	chr14:69863400-69864200	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr14:69863400-69864200	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr14:69863400-69864200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr14:69863400-69864200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr14:69863400-69864200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
33	chr14:69863400-69864200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
34	chr14:69863400-69864200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr14:69863400-69864200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
36	chr14:69863400-69864200	Transcr. at gene 5' and 3'	A549	lung
37	chr14:69863400-69864200	Flanking Active TSS	HUVEC	blood vessel
38	chr14:69863400-69864200	Flanking Active TSS	NHDF-Ad	bronchial
39	chr14:69863400-69864200	Flanking Active TSS	NHEK	skin
40	chr14:69863400-69864200	Flanking Active TSS	NHLF	lung
41	chr14:69863400-69864200	Flanking Active TSS	Osteobl	bone
42	chr14:69863400-69866000	Active TSS	Psoas Muscle	Psoas
43	chr14:69863600-69864000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
44	chr14:69863600-69864000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
45	chr14:69863600-69864000	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr14:69863600-69864000	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr14:69863600-69864200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
48	chr14:69863600-69864200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr14:69863600-69864200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr14:69863600-69864200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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