Variant report

Variant	rs12937232
Chromosome Location	chr17:59820170-59820171
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:59492196..59494427-chr17:59818086..59820888,2	MCF-7	breast:
2	chr17:59782208..59785864-chr17:59818424..59822592,3	MCF-7	breast:

Extended variants
information (count: 137 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs1015771	0.95[CEU][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs10221278	1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes]
rs10438771	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes]
rs10468558	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.81[EUR][1000 genomes]
rs10515206	1.00[CEU][hapmap];0.81[CHB][hapmap];0.80[EUR][1000 genomes]
rs10515207	0.94[CEU][hapmap];0.88[CHB][hapmap]
rs10515211	0.90[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs10853038	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[EUR][1000 genomes]
rs10853039	0.83[EUR][1000 genomes]
rs11079445	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.81[EUR][1000 genomes]
rs11079446	0.82[EUR][1000 genomes]
rs11079448	0.82[EUR][1000 genomes]
rs11650471	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes]
rs11651510	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11653175	0.84[EUR][1000 genomes]
rs11658539	0.84[EUR][1000 genomes]
rs11871753	0.90[CEU][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs12449319	0.82[EUR][1000 genomes]
rs12450027	0.80[EUR][1000 genomes]
rs12451862	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12453293	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12453801	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes]
rs12453935	0.80[MEX][hapmap]
rs12453966	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12603485	0.80[EUR][1000 genomes]
rs12603617	0.85[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[GIH][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes]
rs12948762	0.84[EUR][1000 genomes]
rs12949659	0.90[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs12950438	0.92[EUR][1000 genomes]
rs1468577	0.90[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs1541346	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.80[EUR][1000 genomes]
rs16945500	0.82[EUR][1000 genomes]
rs17532528	0.81[EUR][1000 genomes]
rs1978244	0.90[CEU][hapmap];0.84[GIH][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs1990337	0.84[EUR][1000 genomes]
rs1990338	0.90[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs2024188	0.92[EUR][1000 genomes]
rs2040608	1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.80[EUR][1000 genomes]
rs2109252	0.91[EUR][1000 genomes]
rs2109254	0.91[EUR][1000 genomes]
rs2109255	0.91[EUR][1000 genomes]
rs2159450	0.91[EUR][1000 genomes]
rs2188731	0.80[EUR][1000 genomes]
rs2191247	0.90[EUR][1000 genomes]
rs2191249	0.95[CEU][hapmap];0.84[GIH][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs2214184	0.84[EUR][1000 genomes]
rs2378874	0.80[EUR][1000 genomes]
rs2378875	0.80[EUR][1000 genomes]
rs2378884	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2378902	0.91[EUR][1000 genomes]
rs2378905	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs2378906	0.84[EUR][1000 genomes]
rs28571892	0.92[EUR][1000 genomes]
rs2890012	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[EUR][1000 genomes]
rs2890013	1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[EUR][1000 genomes]
rs2890021	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs36031690	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4309463	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4343344	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4580256	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4968444	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[EUR][1000 genomes]
rs4968447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4968577	0.80[EUR][1000 genomes]
rs4968579	0.82[EUR][1000 genomes]
rs4968580	0.82[EUR][1000 genomes]
rs4968582	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes]
rs4968584	0.82[EUR][1000 genomes]
rs4968585	0.82[EUR][1000 genomes]
rs4968588	0.83[EUR][1000 genomes]
rs4988351	0.85[EUR][1000 genomes]
rs55797010	0.82[EUR][1000 genomes]
rs56284136	0.82[EUR][1000 genomes]
rs57099937	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57393813	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61599541	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62068837	0.84[EUR][1000 genomes]
rs62070615	0.82[EUR][1000 genomes]
rs62070616	0.82[EUR][1000 genomes]
rs62070617	0.82[EUR][1000 genomes]
rs6504066	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs6504068	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs6504070	0.86[EUR][1000 genomes]
rs6504071	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs6504072	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs67273191	0.80[EUR][1000 genomes]
rs67938055	0.82[EUR][1000 genomes]
rs717961	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs717962	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7207074	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7207881	0.95[CEU][hapmap];0.82[JPT][hapmap];0.92[EUR][1000 genomes]
rs7208704	0.94[CEU][hapmap];0.87[JPT][hapmap]
rs7212172	0.90[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs7212423	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7213329	0.90[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs7213470	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7213587	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7213759	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7214884	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs7215784	0.90[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs7216011	0.85[EUR][1000 genomes]
rs7216756	0.90[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs7216824	0.85[EUR][1000 genomes]
rs7217206	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs7217292	0.91[EUR][1000 genomes]
rs7220688	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7220719	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7222799	0.90[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs72841508	0.82[EUR][1000 genomes]
rs8074949	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8075370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8075397	0.92[EUR][1000 genomes]
rs8077088	0.84[EUR][1000 genomes]
rs8078977	0.84[CEU][hapmap];0.89[EUR][1000 genomes]
rs8182296	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9303449	1.00[CEU][hapmap];0.87[CHB][hapmap];0.83[GIH][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes]
rs9807012	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9895987	0.90[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs9896013	0.80[EUR][1000 genomes]
rs9897121	0.90[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs9897450	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9897928	0.95[CEU][hapmap];0.82[JPT][hapmap];0.92[EUR][1000 genomes]
rs9900559	0.84[EUR][1000 genomes]
rs9901428	0.81[EUR][1000 genomes]
rs9902995	0.95[CEU][hapmap];0.84[GIH][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs9903041	0.81[EUR][1000 genomes]
rs9904292	0.90[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs9904294	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9905870	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9906313	0.95[CEU][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs9907299	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs991378	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3378293	chr17:59744117-60124899	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv908673	chr17:59767501-59926645	Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	94 gene(s)	inside rSNPs	diseases
3	nsv908674	chr17:59800827-59899790	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
4	esv3335472	chr17:59803168-59821322	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv575841	chr17:59812748-59914681	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
6	nsv575842	chr17:59812748-59927307	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12937232	DYNLL2	cis	cerebellum	SCAN
rs12937232	BRIP1	cis	parietal	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59781600-59835400	Weak transcription	Hela-S3	cervix
2	chr17:59793600-59821200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr17:59794400-59848200	Weak transcription	HUVEC	blood vessel
4	chr17:59804200-59847400	Weak transcription	K562	blood
5	chr17:59804600-59834200	Weak transcription	Osteobl	bone
6	chr17:59806200-59825600	Weak transcription	Thymus	Thymus
7	chr17:59807600-59838400	Weak transcription	Fetal Stomach	stomach
8	chr17:59811600-59825200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr17:59813600-59821000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr17:59813800-59820400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr17:59813800-59823000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr17:59814000-59849000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr17:59814600-59823000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr17:59815000-59824000	Weak transcription	Fetal Heart	heart
15	chr17:59815000-59839200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr17:59815200-59820200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
17	chr17:59815200-59820200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr17:59815200-59820400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr17:59815400-59820400	Strong transcription	Fetal Thymus	thymus
20	chr17:59815600-59828200	Weak transcription	NHLF	lung
21	chr17:59815600-59836000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr17:59815600-59844200	Weak transcription	HMEC	breast
23	chr17:59815800-59834400	Weak transcription	HSMM	muscle
24	chr17:59815800-59843400	Weak transcription	NHEK	skin
25	chr17:59816200-59820200	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr17:59816400-59820400	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr17:59816800-59887800	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr17:59817800-59820200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr17:59818000-59820400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr17:59818000-59820600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
31	chr17:59818000-59820600	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr17:59818200-59820600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr17:59818200-59821000	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr17:59818200-59823400	Weak transcription	Primary T cells from cord blood	blood
35	chr17:59818400-59820200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr17:59818400-59820400	Strong transcription	A549	lung
37	chr17:59818400-59821800	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr17:59818800-59820400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr17:59819000-59820400	ZNF genes & repeats	GM12878-XiMat	blood
40	chr17:59819000-59842600	Weak transcription	Fetal Muscle Trunk	muscle
41	chr17:59819200-59820200	Strong transcription	Fetal Lung	lung
42	chr17:59819400-59820400	Strong transcription	Fetal Intestine Large	intestine
43	chr17:59819400-59820400	Strong transcription	NH-A	brain
44	chr17:59819400-59843600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr17:59819400-59848200	Weak transcription	Primary B cells from cord blood	blood
46	chr17:59819600-59820400	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr17:59819600-59820400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr17:59819600-59820800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr17:59819600-59821400	Strong transcription	HepG2	liver
50	chr17:59819600-59823000	Strong transcription	Monocytes-CD14+_RO01746	blood

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