Variant report

Variant	rs3999570
Chromosome Location	chr10:61603218-61603219
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:61603087..61604975-chr10:61665776..61667590,2	MCF-7	breast:
2	chr10:61603038..61604837-chr10:61615583..61618517,2	K562	blood:

Variant related genes	Relation type
ENSG00000108091	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10458645	0.85[CEU][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10509112	0.85[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap]
rs10821604	0.85[CEU][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10821605	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10821606	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10821607	0.82[CEU][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10994021	0.85[JPT][hapmap]
rs10994022	0.82[JPT][hapmap]
rs10994026	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs10994027	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs10994030	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs10994031	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs10994051	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1149660	0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs1149661	0.85[ASN][1000 genomes]
rs1149662	0.85[ASN][1000 genomes]
rs1149663	0.84[ASN][1000 genomes]
rs1171786	0.81[ASW][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.82[MEX][hapmap];0.86[ASN][1000 genomes]
rs1171788	0.91[ASN][1000 genomes]
rs1177701	0.81[CEU][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes]
rs12243564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12244844	0.81[ASN][1000 genomes]
rs12252428	0.82[ASN][1000 genomes]
rs12259529	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs12262735	0.85[CHB][hapmap]
rs12266466	0.87[ASN][1000 genomes]
rs1621496	0.81[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs1664255	0.93[ASN][1000 genomes]
rs1664256	0.88[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs1664284	0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.97[ASN][1000 genomes]
rs1664285	0.94[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs1684896	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1684901	0.85[JPT][hapmap]
rs1684929	0.83[ASN][1000 genomes]
rs16914233	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs1709342	0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs1709343	0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs1709344	0.84[ASN][1000 genomes]
rs1709345	0.83[CEU][hapmap];0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1871637	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1871638	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2120989	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2120990	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2271562	0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs2440926	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs2458661	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2458663	0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.97[ASN][1000 genomes]
rs2458664	0.82[ASN][1000 genomes]
rs3106569	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3793878	0.85[JPT][hapmap]
rs3844161	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3851247	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3851248	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3862860	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3862861	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3999569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4948244	0.85[CHB][hapmap];0.84[CHD][hapmap]
rs4948372	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4948373	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4948374	0.91[ASW][hapmap];0.96[CEU][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4948375	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55706286	0.81[ASN][1000 genomes]
rs55842846	0.95[ASN][1000 genomes]
rs57348988	0.82[ASN][1000 genomes]
rs61848702	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6479653	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs6479654	0.85[CEU][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6479657	0.92[ASN][1000 genomes]
rs6479658	0.83[ASN][1000 genomes]
rs6479659	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6479660	0.94[ASN][1000 genomes]
rs6479661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479662	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7068104	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7068247	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7070800	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7074685	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7078533	0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs7079228	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7079588	0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs7080447	0.82[ASN][1000 genomes]
rs7088755	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs7088808	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7088886	0.90[CHD][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap];0.80[ASN][1000 genomes]
rs7092259	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs72817923	0.81[ASN][1000 genomes]
rs7908517	0.85[CEU][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7910256	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs7920049	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs7920403	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9663498	0.91[ASW][hapmap];1.00[CEU][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9664183	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3999570	HOXA4	trans	parietal	SCAN
rs3999570	EGR2	cis	parietal	SCAN
rs3999570	SLC16A9	cis	parietal	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:61571400-61628000	Weak transcription	Spleen	Spleen
2	chr10:61571600-61609200	Weak transcription	NHLF	lung
3	chr10:61571600-61616000	Weak transcription	Fetal Kidney	kidney
4	chr10:61572000-61615000	Weak transcription	Colonic Mucosa	Colon
5	chr10:61572400-61618800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr10:61578000-61623200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr10:61578400-61603400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr10:61580200-61605600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr10:61580200-61624200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr10:61580400-61624200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr10:61580600-61616200	Weak transcription	Fetal Brain Male	brain
12	chr10:61583200-61606600	Weak transcription	Pancreas	Pancrea
13	chr10:61583200-61640600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr10:61584400-61607200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr10:61586000-61605600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr10:61586000-61612200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr10:61586400-61606600	Weak transcription	Gastric	stomach
18	chr10:61586400-61606800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr10:61587000-61612000	Weak transcription	Ovary	ovary
20	chr10:61589400-61616200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr10:61591600-61609400	Weak transcription	Brain Germinal Matrix	brain
22	chr10:61591800-61607200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr10:61591800-61607600	Weak transcription	A549	lung
24	chr10:61591800-61609000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr10:61591800-61624000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr10:61592200-61605400	Weak transcription	Adipose Nuclei	Adipose
27	chr10:61592400-61605200	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr10:61592400-61605400	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr10:61592400-61605600	Weak transcription	Liver	Liver
30	chr10:61592400-61607600	Weak transcription	Fetal Lung	lung
31	chr10:61592600-61603400	Weak transcription	Dnd41	blood
32	chr10:61592600-61605400	Weak transcription	HepG2	liver
33	chr10:61592600-61605600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr10:61592600-61608800	Weak transcription	HUVEC	blood vessel
35	chr10:61592600-61616600	Weak transcription	NH-A	brain
36	chr10:61593200-61629400	Weak transcription	Lung	lung
37	chr10:61594000-61606600	Weak transcription	Right Ventricle	heart
38	chr10:61594000-61614000	Weak transcription	Small Intestine	intestine
39	chr10:61595200-61607200	Weak transcription	Thymus	Thymus
40	chr10:61595200-61614000	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr10:61595800-61607200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr10:61595800-61624000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr10:61596000-61603600	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr10:61596000-61607200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr10:61596000-61607200	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr10:61596000-61607600	Weak transcription	Colon Smooth Muscle	Colon
47	chr10:61596000-61612000	Weak transcription	Rectal Smooth Muscle	rectum
48	chr10:61596200-61603400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr10:61596200-61603400	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr10:61596200-61603400	Weak transcription	Primary T helper cells PMA-I stimulated	--

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