Variant report

Variant	rs2964574
Chromosome Location	chr5:151155711-151155712
allele	C/T
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	chr5:151155504-151156003	GM12878	blood:	n/a	n/a
2	POLR2A	chr5:151155606-151155806	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr5:151154534-151155822	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr5:151154120-151156141	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:151153858..151156919-chr5:151169412..151173368,3	K562	blood:

Variant related genes	Relation type
ATOX1	TF binding region

Extended variants
information (count: 106 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10044368	0.94[CHB][hapmap];0.87[CHD][hapmap];0.82[ASN][1000 genomes]
rs10075101	0.82[ASN][1000 genomes]
rs1042877	0.94[CHB][hapmap];0.87[CHD][hapmap];0.82[ASN][1000 genomes]
rs1062177	0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10875569	0.83[ASN][1000 genomes]
rs12108921	0.87[CHB][hapmap]
rs12109022	0.87[CHB][hapmap]
rs12515762	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12654573	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12654877	0.82[ASN][1000 genomes]
rs1433041	0.94[CHB][hapmap];0.87[CHD][hapmap];0.82[ASN][1000 genomes]
rs1549920	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1549921	0.83[ASN][1000 genomes]
rs17741826	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17804178	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1972780	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1978710	0.85[ASN][1000 genomes]
rs2016409	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2053063	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2347596	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2347597	0.94[CHB][hapmap];0.87[CHD][hapmap];0.82[ASN][1000 genomes]
rs2913889	0.87[CHB][hapmap]
rs2913892	0.87[CHB][hapmap]
rs2913893	0.87[CHB][hapmap]
rs2913894	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs2915815	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2915816	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2915817	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2915818	0.95[ASN][1000 genomes]
rs2915820	0.92[ASN][1000 genomes]
rs2915822	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2915823	0.80[ASN][1000 genomes]
rs2915824	0.80[ASN][1000 genomes]
rs2915826	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2915827	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2915828	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2915829	0.82[ASN][1000 genomes]
rs2915868	0.94[CHB][hapmap];0.87[CHD][hapmap];0.82[ASN][1000 genomes]
rs2915869	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2915870	0.82[ASN][1000 genomes]
rs2915871	0.83[ASN][1000 genomes]
rs2915872	0.94[CHB][hapmap];0.90[CHD][hapmap];0.84[ASN][1000 genomes]
rs2915873	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2915874	0.80[ASN][1000 genomes]
rs2915876	0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2915877	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2915878	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2915879	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2915880	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2915881	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2915882	0.90[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2915883	0.82[ASN][1000 genomes]
rs2915886	0.88[CHB][hapmap]
rs2915887	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2915888	0.94[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs2915890	0.93[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs2915891	0.82[ASN][1000 genomes]
rs2915892	0.82[ASN][1000 genomes]
rs2915893	0.82[ASN][1000 genomes]
rs2915894	0.82[ASN][1000 genomes]
rs2964568	0.81[ASN][1000 genomes]
rs2964570	0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs2964571	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2964572	0.82[ASN][1000 genomes]
rs2964573	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2964576	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2964577	0.80[ASN][1000 genomes]
rs2964578	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2964580	0.83[ASN][1000 genomes]
rs2964581	0.83[ASN][1000 genomes]
rs2964582	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2964583	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2964584	0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2964585	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2964587	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2964588	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2964589	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2964590	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2964591	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2964592	0.95[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2964593	0.94[ASN][1000 genomes]
rs2964594	0.86[ASN][1000 genomes]
rs2964595	0.87[ASN][1000 genomes]
rs2964610	0.83[ASN][1000 genomes]
rs2964611	0.84[ASN][1000 genomes]
rs2964612	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2964613	0.86[ASN][1000 genomes]
rs4472253	0.82[ASN][1000 genomes]
rs4571461	0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs4629586	0.82[ASN][1000 genomes]
rs62377931	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62377945	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6579897	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6579901	0.91[ASN][1000 genomes]
rs6878198	0.85[ASN][1000 genomes]
rs6879461	0.82[ASN][1000 genomes]
rs6890099	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72802204	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7719617	0.94[CHB][hapmap]
rs7720579	0.82[ASN][1000 genomes]
rs7728956	0.85[CHB][hapmap]
rs7733241	0.87[CHB][hapmap]
rs7734314	0.94[CHB][hapmap];0.87[CHD][hapmap];0.82[ASN][1000 genomes]
rs892005	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs892006	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs973529	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2964574	RP11-54C4.1	cis	Nerve Tibial	GTEx
rs2964574	RP11-54C4.1	cis	Thyroid	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:151152200-151156000	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr5:151152800-151160000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:151152800-151163000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr5:151153000-151157200	Weak transcription	Left Ventricle	heart
5	chr5:151153000-151160000	Weak transcription	Gastric	stomach
6	chr5:151153000-151167400	Weak transcription	Esophagus	oesophagus
7	chr5:151153000-151167400	Weak transcription	Lung	lung
8	chr5:151153000-151167600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr5:151153200-151155800	Enhancers	Primary B cells from peripheral blood	blood
10	chr5:151153400-151156600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr5:151153800-151155800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr5:151153800-151155800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
13	chr5:151153800-151155800	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr5:151153800-151155800	Enhancers	Fetal Brain Male	brain
15	chr5:151153800-151156000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr5:151153800-151157200	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr5:151153800-151160400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr5:151153800-151162000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr5:151153800-151165200	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr5:151153800-151166800	Weak transcription	Colonic Mucosa	Colon
21	chr5:151153800-151167400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr5:151153800-151169800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr5:151154000-151155800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr5:151154000-151156000	Enhancers	Brain Hippocampus Middle	brain
25	chr5:151154000-151156000	Enhancers	Fetal Intestine Small	intestine
26	chr5:151154000-151156200	Enhancers	Brain Anterior Caudate	brain
27	chr5:151154000-151156200	Enhancers	Brain Cingulate Gyrus	brain
28	chr5:151154000-151156200	Enhancers	Brain Substantia Nigra	brain
29	chr5:151154000-151156200	Enhancers	Rectal Smooth Muscle	rectum
30	chr5:151154000-151156600	Enhancers	Adipose Nuclei	Adipose
31	chr5:151154000-151156800	Enhancers	Fetal Lung	lung
32	chr5:151154000-151157600	Enhancers	Colon Smooth Muscle	Colon
33	chr5:151154000-151157600	Enhancers	Fetal Heart	heart
34	chr5:151154000-151158000	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr5:151154200-151155800	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr5:151154200-151155800	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr5:151154400-151155800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr5:151154400-151155800	Enhancers	Primary T cells from cord blood	blood
39	chr5:151154400-151155800	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr5:151154400-151155800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr5:151154400-151156400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr5:151154400-151156800	Enhancers	Liver	Liver
43	chr5:151154400-151157400	Weak transcription	Placenta	Placenta
44	chr5:151154400-151168800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr5:151154400-151169000	Weak transcription	HSMMtube	muscle
46	chr5:151154600-151155800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr5:151154600-151155800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr5:151154600-151156600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr5:151154600-151156600	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr5:151154600-151168800	Weak transcription	Placenta Amnion	Placenta Amnion

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