Variant report

Variant	rs12602129
Chromosome Location	chr17:16967340-16967341
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:16955910..16958218-chr17:16967140..16970023,2	MCF-7	breast:
2	chr17:16962310..16965177-chr17:16967176..16969489,2	MCF-7	breast:
3	chr17:16958058..16960902-chr17:16966512..16968421,3	MCF-7	breast:
4	chr17:16966782..16968541-chr17:16972398..16974708,2	MCF-7	breast:

Extended variants
information (count: 102 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs1047805	0.90[AMR][1000 genomes]
rs10852843	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10852844	0.95[AMR][1000 genomes]
rs10852845	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10852846	0.90[AMR][1000 genomes]
rs11078364	0.93[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11078365	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11078366	1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs11078370	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];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11078371	0.95[AMR][1000 genomes]
rs11078372	0.95[AMR][1000 genomes]
rs11078373	0.90[AMR][1000 genomes]
rs11078375	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1110504	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1110505	0.90[AMR][1000 genomes]
rs11651460	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11651938	0.90[AMR][1000 genomes]
rs11651988	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11652079	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11652674	0.87[EUR][1000 genomes]
rs11652678	0.90[AMR][1000 genomes]
rs11652756	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11652936	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11654247	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11654360	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11654562	0.90[CHB][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11658084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11658904	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12450109	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12450213	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12450238	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12450467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12451054	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12452303	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12452802	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12601325	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12602124	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12602867	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16961288	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs16961412	1.00[CHB][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes]
rs1877631	1.00[CHB][hapmap]
rs2292526	0.86[AMR][1000 genomes]
rs3744125	0.90[AMR][1000 genomes]
rs3744127	0.90[AMR][1000 genomes]
rs3744132	0.90[AMR][1000 genomes]
rs3744133	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3744136	0.90[AMR][1000 genomes]
rs3744140	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3826305	0.88[AMR][1000 genomes]
rs4073940	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4074611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4074612	0.87[YRI][hapmap];0.95[AMR][1000 genomes]
rs4074819	0.90[AMR][1000 genomes]
rs4264448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4275916	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4283273	0.90[AMR][1000 genomes]
rs4321246	0.86[AMR][1000 genomes]
rs4606773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4621033	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4985695	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4985697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4985698	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4985703	0.90[AMR][1000 genomes]
rs4985712	0.92[ASN][1000 genomes]
rs4985714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4985715	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985719	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4985723	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4985727	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4985739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4985744	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4985747	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55751545	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56009207	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57812549	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs58326998	0.90[AMR][1000 genomes]
rs58472573	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58814183	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59394251	0.90[AMR][1000 genomes]
rs60128647	0.95[AMR][1000 genomes]
rs61018209	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6502564	0.86[YRI][hapmap]
rs7207187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7210339	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7217970	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7223583	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7223686	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7223924	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73979053	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73979054	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73979055	0.96[AFR][1000 genomes]
rs73979058	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73979060	0.95[AMR][1000 genomes]
rs73979061	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73979081	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73979082	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73979083	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8064991	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8066111	0.90[AMR][1000 genomes]
rs8067563	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8075751	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9910011	0.92[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12602129	M-RIP	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16949000-16975200	Weak transcription	K562	blood
2	chr17:16950200-16968200	Enhancers	Psoas Muscle	Psoas
3	chr17:16952600-16996400	Weak transcription	Fetal Brain Male	brain
4	chr17:16953600-16967600	Genic enhancers	Fetal Muscle Trunk	muscle
5	chr17:16954800-16981200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr17:16955400-16970200	Weak transcription	NH-A	brain
7	chr17:16955400-16981200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr17:16956400-16972600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr17:16959200-16982200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr17:16959400-16972800	Weak transcription	HUVEC	blood vessel
11	chr17:16959600-16979800	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr17:16959600-16992000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr17:16960200-16967600	Genic enhancers	Fetal Muscle Leg	muscle
14	chr17:16960600-16967600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr17:16960800-16976400	Weak transcription	Aorta	Aorta
16	chr17:16961000-16968200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr17:16961000-16970600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr17:16961200-16967400	Genic enhancers	Spleen	Spleen
19	chr17:16961600-16967600	Genic enhancers	Esophagus	oesophagus
20	chr17:16961600-16968400	Enhancers	Right Ventricle	heart
21	chr17:16961600-16977200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr17:16961800-16968400	Enhancers	Brain Anterior Caudate	brain
23	chr17:16962000-16967600	Enhancers	Ovary	ovary
24	chr17:16962000-16968800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr17:16962200-16968000	Strong transcription	Fetal Stomach	stomach
26	chr17:16962600-16968600	Enhancers	Brain Hippocampus Middle	brain
27	chr17:16962800-16968000	Enhancers	Left Ventricle	heart
28	chr17:16962800-16968200	Enhancers	Adipose Nuclei	Adipose
29	chr17:16962800-16968400	Genic enhancers	A549	lung
30	chr17:16963000-16967600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr17:16963200-16968000	Enhancers	Right Atrium	heart
32	chr17:16963200-16968400	Enhancers	Brain Cingulate Gyrus	brain
33	chr17:16963400-16967600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr17:16963400-16968200	Enhancers	Liver	Liver
35	chr17:16963600-16967400	Genic enhancers	Sigmoid Colon	Sigmoid Colon
36	chr17:16963600-16967600	Genic enhancers	HMEC	breast
37	chr17:16963800-16967600	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr17:16963800-16968000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr17:16964200-16967600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr17:16964400-16967400	Genic enhancers	Fetal Intestine Small	intestine
41	chr17:16964400-16967600	Genic enhancers	Fetal Intestine Large	intestine
42	chr17:16964400-16973600	Weak transcription	HepG2	liver
43	chr17:16964400-16974200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr17:16964800-16967400	Enhancers	Stomach Mucosa	stomach
45	chr17:16964800-16968000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr17:16964800-16968000	Genic enhancers	NHLF	lung
47	chr17:16964800-16968400	Genic enhancers	Osteobl	bone
48	chr17:16964800-16969600	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr17:16965000-16967400	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr17:16965000-16967400	Enhancers	Placenta	Placenta

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