Variant report

Variant	rs10852844
Chromosome Location	chr17:17009331-17009332
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17008907..17011801-chr17:17020811..17022736,2	K562	blood:
2	chr17:17008754..17011646-chr17:17017494..17019040,2	MCF-7	breast:
3	chr17:17005653..17007729-chr17:17008275..17010821,3	MCF-7	breast:
4	chr17:17001973..17004582-chr17:17006426..17009352,2	MCF-7	breast:

Extended variants
information (count: 152 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:151)

rs_ID	r²[population]
rs1047799	0.94[CHB][hapmap];1.00[CHD][hapmap]
rs1047805	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10852843	0.95[AMR][1000 genomes]
rs10852845	0.95[AMR][1000 genomes]
rs10852846	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11078364	0.88[AMR][1000 genomes]
rs11078365	0.93[AMR][1000 genomes]
rs11078366	0.88[MEX][hapmap]
rs11078368	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11078370	0.95[AMR][1000 genomes]
rs11078371	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11078372	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11078373	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11078375	0.90[AMR][1000 genomes]
rs1110504	0.90[AMR][1000 genomes]
rs1110505	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11551189	0.87[ASN][1000 genomes]
rs11651460	1.00[MEX][hapmap];0.90[AMR][1000 genomes]
rs11651938	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11651988	0.95[AMR][1000 genomes]
rs11652079	0.90[AMR][1000 genomes]
rs11652678	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11652756	0.95[AMR][1000 genomes]
rs11652936	0.95[AMR][1000 genomes]
rs11654247	0.90[AMR][1000 genomes]
rs11654360	0.90[AMR][1000 genomes]
rs11654562	0.93[AMR][1000 genomes]
rs11654887	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11657189	0.91[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11658084	1.00[MEX][hapmap];0.95[AMR][1000 genomes]
rs11870035	0.88[ASN][1000 genomes]
rs11870483	0.97[ASN][1000 genomes]
rs12450109	0.95[AMR][1000 genomes]
rs12450213	0.93[AMR][1000 genomes]
rs12450238	0.93[AMR][1000 genomes]
rs12450467	0.95[AMR][1000 genomes]
rs12451054	0.95[AMR][1000 genomes]
rs12451343	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12452802	0.90[AMR][1000 genomes]
rs12601325	0.90[AMR][1000 genomes]
rs12601422	0.94[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs12602129	0.95[AMR][1000 genomes]
rs12602583	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12602592	0.91[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12602839	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12602867	0.90[AMR][1000 genomes]
rs12603417	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1567815	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16961288	0.95[AMR][1000 genomes]
rs16961412	1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs17794784	0.94[CHB][hapmap];0.83[ASN][1000 genomes]
rs1877631	0.88[MEX][hapmap]
rs2292526	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2292530	0.94[CHB][hapmap];1.00[CHD][hapmap];0.83[ASN][1000 genomes]
rs2349645	0.88[ASN][1000 genomes]
rs2349648	0.97[ASN][1000 genomes]
rs28452405	0.96[ASN][1000 genomes]
rs34001712	0.96[ASN][1000 genomes]
rs34976658	0.80[ASN][1000 genomes]
rs35650871	0.92[ASN][1000 genomes]
rs3744125	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3744127	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3744131	0.94[CHB][hapmap];0.87[ASN][1000 genomes]
rs3744132	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3744133	1.00[MEX][hapmap];0.90[AMR][1000 genomes]
rs3744134	0.94[CHB][hapmap];0.97[CHD][hapmap];0.83[ASN][1000 genomes]
rs3744136	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3744137	0.94[CHB][hapmap];1.00[CHD][hapmap];0.88[ASN][1000 genomes]
rs3744138	0.89[CHB][hapmap];1.00[CHD][hapmap];0.88[ASN][1000 genomes]
rs3744139	0.94[CHB][hapmap];1.00[CHD][hapmap];0.88[ASN][1000 genomes]
rs3744140	1.00[MEX][hapmap];0.90[AMR][1000 genomes]
rs3826305	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4073688	0.91[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4073940	0.81[MEX][hapmap]
rs4074611	0.95[AMR][1000 genomes]
rs4074612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4074819	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4264448	0.95[AMR][1000 genomes]
rs4275916	0.95[AMR][1000 genomes]
rs4283273	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4321246	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4468683	0.87[ASN][1000 genomes]
rs4606773	1.00[MEX][hapmap];0.95[AMR][1000 genomes]
rs4621033	0.95[AMR][1000 genomes]
rs4629023	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4641803	0.83[ASN][1000 genomes]
rs4985695	0.95[AMR][1000 genomes]
rs4985697	0.95[AMR][1000 genomes]
rs4985698	0.95[AMR][1000 genomes]
rs4985703	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4985704	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4985714	1.00[MEX][hapmap];0.95[AMR][1000 genomes]
rs4985716	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4985719	0.95[AMR][1000 genomes]
rs4985721	0.96[ASN][1000 genomes]
rs4985727	0.95[AMR][1000 genomes]
rs4985728	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4985730	0.97[ASN][1000 genomes]
rs4985737	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs4985739	1.00[MEX][hapmap];0.90[AMR][1000 genomes]
rs4985741	0.94[CHB][hapmap];1.00[CHD][hapmap];0.80[ASN][1000 genomes]
rs4985742	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4985743	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4985744	0.90[AMR][1000 genomes]
rs4985745	0.80[ASN][1000 genomes]
rs4985747	0.86[AMR][1000 genomes]
rs55751545	0.90[AMR][1000 genomes]
rs56009207	0.95[AMR][1000 genomes]
rs56133536	0.88[ASN][1000 genomes]
rs57729820	0.94[ASN][1000 genomes]
rs57812549	0.88[AMR][1000 genomes]
rs58326998	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58472573	0.95[AMR][1000 genomes]
rs58814183	0.95[AMR][1000 genomes]
rs59394251	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60128647	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61018209	0.90[AMR][1000 genomes]
rs61242604	0.89[ASN][1000 genomes]
rs7207187	0.95[AMR][1000 genomes]
rs7210339	0.95[AMR][1000 genomes]
rs7211576	0.80[ASN][1000 genomes]
rs7212275	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7214429	0.94[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs7216677	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7217970	1.00[MEX][hapmap];0.90[AMR][1000 genomes]
rs7218781	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];0.92[TSI][hapmap];0.81[YRI][hapmap]
rs7223583	0.95[AMR][1000 genomes]
rs73979053	0.88[AMR][1000 genomes]
rs73979054	0.95[AMR][1000 genomes]
rs73979058	0.95[AMR][1000 genomes]
rs73979060	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73979061	0.95[AMR][1000 genomes]
rs73979078	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73979081	0.95[AMR][1000 genomes]
rs73979082	0.95[AMR][1000 genomes]
rs73979083	0.95[AMR][1000 genomes]
rs8064991	0.90[AMR][1000 genomes]
rs8066111	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8066234	0.94[CHB][hapmap];1.00[CHD][hapmap];0.80[ASN][1000 genomes]
rs8067563	0.95[AMR][1000 genomes]
rs8069259	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8071254	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8075751	0.88[MEX][hapmap]
rs8076273	0.83[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs8077360	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9892695	0.83[ASN][1000 genomes]
rs9893676	0.87[ASN][1000 genomes]
rs9897510	0.87[ASN][1000 genomes]
rs9906028	0.92[ASN][1000 genomes]
rs9907109	0.94[ASN][1000 genomes]
rs9910857	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059280	chr17:16975059-17017957	Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10852844	PLD6	cis	lymphoblastoid	seeQTL
rs10852844	M-RIP	cis	multi-tissue	Pritchard
rs10852844	MPRIP	cis	lymphoblastoid	seeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16986800-17013600	Weak transcription	HUVEC	blood vessel
2	chr17:16992400-17010000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr17:16993400-17011400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr17:16994600-17011600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr17:16997000-17016600	Enhancers	Left Ventricle	heart
6	chr17:16997400-17010000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr17:16998200-17016200	Enhancers	Fetal Heart	heart
8	chr17:16998600-17015400	Genic enhancers	Fetal Muscle Leg	muscle
9	chr17:16998600-17016600	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr17:16999000-17012800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr17:17000200-17012600	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr17:17000200-17018200	Weak transcription	NH-A	brain
13	chr17:17000600-17009800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr17:17000600-17009800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr17:17001600-17010200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr17:17001600-17010800	Weak transcription	Aorta	Aorta
17	chr17:17001600-17011400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr17:17001800-17009800	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr17:17001800-17012800	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr17:17002000-17010200	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr17:17002000-17010600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr17:17002000-17010600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr17:17002000-17011400	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr17:17002400-17011600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr17:17002600-17009400	Weak transcription	Stomach Mucosa	stomach
26	chr17:17002600-17009800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr17:17002600-17010800	Weak transcription	Brain Germinal Matrix	brain
28	chr17:17002600-17011200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr17:17002600-17011400	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr17:17002600-17012000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr17:17002600-17023200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr17:17002800-17011600	Weak transcription	Small Intestine	intestine
33	chr17:17003000-17009600	Strong transcription	Osteobl	bone
34	chr17:17003000-17010000	Weak transcription	Fetal Kidney	kidney
35	chr17:17003000-17010800	Genic enhancers	Fetal Muscle Trunk	muscle
36	chr17:17003400-17009400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr17:17003400-17012600	Weak transcription	Fetal Brain Male	brain
38	chr17:17004000-17009600	Strong transcription	Primary T cells from cord blood	blood
39	chr17:17004000-17010400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr17:17004000-17014000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr17:17004400-17009400	Strong transcription	A549	lung
42	chr17:17004400-17009800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr17:17004400-17010400	Weak transcription	HSMMtube	muscle
44	chr17:17004400-17010600	Weak transcription	Colonic Mucosa	Colon
45	chr17:17004600-17010000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr17:17005800-17009600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr17:17006200-17009600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr17:17006200-17009600	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr17:17006200-17009800	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr17:17006200-17033000	Weak transcription	Primary neutrophils fromperipheralblood	blood

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