Variant report

Variant	rs2970599
Chromosome Location	chr1:212183497-212183498
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212181923..212184932-chr1:212207309..212210434,3	K562	blood:
2	chr1:212178489..212180435-chr1:212181664..212184170,2	K562	blood:
3	chr1:212177757..212179795-chr1:212180730..212183716,2	MCF-7	breast:
4	chr1:212181923..212187043-chr1:212203247..212211054,10	K562	blood:
5	chr1:212175644..212177719-chr1:212180897..212183768,2	K562	blood:

Variant related genes	Relation type
ENSG00000143493	Chromatin interaction
ENSG00000143476	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11119839	0.80[ASN][1000 genomes]
rs11119840	0.80[ASN][1000 genomes]
rs11119843	0.80[JPT][hapmap]
rs12070369	0.84[JPT][hapmap]
rs1316820	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1578992	0.91[JPT][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes]
rs1578993	0.89[ASW][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap];0.86[YRI][hapmap]
rs1933593	0.94[ASW][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.85[MKK][hapmap];0.89[YRI][hapmap]
rs2014029	0.82[JPT][hapmap]
rs2105162	0.89[ASN][1000 genomes]
rs2130503	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2248191	0.82[JPT][hapmap]
rs2358386	0.94[ASW][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.82[MKK][hapmap];0.90[YRI][hapmap]
rs2358440	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2788139	0.86[JPT][hapmap]
rs2788140	0.89[ASW][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap]
rs2808392	0.95[JPT][hapmap];0.90[YRI][hapmap];0.80[ASN][1000 genomes]
rs2884428	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2970592	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2970601	0.95[JPT][hapmap];0.86[YRI][hapmap];0.87[ASN][1000 genomes]
rs2993528	0.88[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2993529	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2993531	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2993533	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2993534	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2993544	0.95[JPT][hapmap];0.86[YRI][hapmap];0.87[ASN][1000 genomes]
rs3009985	0.85[ASN][1000 genomes]
rs3010003	1.00[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];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3010004	0.86[JPT][hapmap]
rs3010006	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3010023	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3010024	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3738449	0.94[ASW][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.85[LWK][hapmap];0.85[MKK][hapmap];0.81[TSI][hapmap];0.90[YRI][hapmap]
rs4951435	0.97[ASN][1000 genomes]
rs4951560	0.82[JPT][hapmap]
rs4951561	0.82[JPT][hapmap]
rs6657728	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs6684814	0.91[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2970599	PROX1	cis	cerebellum	SCAN
rs2970599	INTS7	Cis_1M	lymphoblastoid	RTeQTL
rs2970599	C1orf74	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212112800-212202000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr1:212114200-212185800	Weak transcription	Brain Angular Gyrus	brain
3	chr1:212123800-212198200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr1:212129400-212204000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:212133400-212188200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:212133800-212208000	Weak transcription	Gastric	stomach
7	chr1:212134000-212207600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr1:212134000-212207800	Weak transcription	Colonic Mucosa	Colon
9	chr1:212136600-212204000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:212146000-212185600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr1:212148800-212207600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr1:212149200-212199800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:212151800-212187000	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr1:212152800-212201600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr1:212153400-212203600	Weak transcription	Psoas Muscle	Psoas
16	chr1:212153600-212202600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr1:212160000-212189400	Weak transcription	NHDF-Ad	bronchial
18	chr1:212160200-212199800	Weak transcription	Brain Substantia Nigra	brain
19	chr1:212160200-212202600	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr1:212161200-212189200	Weak transcription	NH-A	brain
21	chr1:212168800-212185200	Strong transcription	Fetal Thymus	thymus
22	chr1:212170000-212184600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:212170200-212191400	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr1:212170200-212197600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr1:212170400-212185000	Strong transcription	Dnd41	blood
26	chr1:212170400-212202600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr1:212170600-212194200	Weak transcription	Placenta	Placenta
28	chr1:212170800-212199200	Weak transcription	Pancreas	Pancrea
29	chr1:212170800-212207800	Weak transcription	Right Ventricle	heart
30	chr1:212171000-212188200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr1:212171000-212189400	Weak transcription	Brain Anterior Caudate	brain
32	chr1:212171000-212199800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr1:212171200-212189800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:212171200-212197800	Weak transcription	Brain Cingulate Gyrus	brain
35	chr1:212171200-212208000	Weak transcription	Esophagus	oesophagus
36	chr1:212171200-212208000	Weak transcription	Lung	lung
37	chr1:212171400-212197800	Weak transcription	Aorta	Aorta
38	chr1:212171600-212185400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:212171600-212189400	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr1:212171600-212198000	Weak transcription	Fetal Kidney	kidney
41	chr1:212171600-212198200	Weak transcription	Small Intestine	intestine
42	chr1:212171600-212207400	Weak transcription	Fetal Stomach	stomach
43	chr1:212171800-212188000	Weak transcription	Fetal Intestine Small	intestine
44	chr1:212171800-212191400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr1:212171800-212197600	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr1:212171800-212207600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr1:212172200-212199800	Weak transcription	Stomach Mucosa	stomach
48	chr1:212173000-212204200	Weak transcription	Fetal Heart	heart
49	chr1:212173800-212184800	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr1:212174000-212185200	Strong transcription	GM12878-XiMat	blood

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