Variant report

Variant	rs17757522
Chromosome Location	chr4:147103739-147103740
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:147103664-147104035	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:147095588..147099041-chr4:147101501..147104102,4	MCF-7	breast:

Variant related genes	Relation type
LSM6	TF binding region
ENSG00000164167	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10000407	0.84[EUR][1000 genomes]
rs10017509	0.88[CEU][hapmap]
rs10519776	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1079476	0.98[ASN][1000 genomes]
rs11100919	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11721367	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11721873	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11722991	0.88[CEU][hapmap]
rs11723069	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11724307	0.86[EUR][1000 genomes]
rs11724732	1.00[YRI][hapmap]
rs11725678	0.83[EUR][1000 genomes]
rs11728525	0.86[EUR][1000 genomes]
rs11728609	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11729787	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11730306	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11733347	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11734320	0.88[CEU][hapmap]
rs11940961	0.96[CEU][hapmap];0.82[CHB][hapmap];0.82[EUR][1000 genomes]
rs12152657	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12152692	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12152709	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12186313	0.88[CEU][hapmap]
rs17021186	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17021217	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17021239	0.85[CEU][hapmap]
rs17021241	0.86[CEU][hapmap]
rs17756056	0.84[EUR][1000 genomes]
rs17756234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17757685	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17757715	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17758092	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17758396	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17758420	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17814023	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17814065	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17814503	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17814598	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1864371	0.96[CEU][hapmap];0.82[CHB][hapmap];0.83[EUR][1000 genomes]
rs1865531	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2007366	0.84[EUR][1000 genomes]
rs2068009	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2115796	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2115797	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2163171	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2164280	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28393640	0.83[EUR][1000 genomes]
rs28420466	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733458	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733459	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3733460	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3733461	0.88[CEU][hapmap]
rs3756081	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756082	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756083	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775498	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3815967	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3948408	0.83[EUR][1000 genomes]
rs4282199	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4549398	0.83[EUR][1000 genomes]
rs4835283	0.88[CEU][hapmap]
rs4835284	0.88[CEU][hapmap]
rs4835286	0.96[CEU][hapmap];0.82[CHB][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs55736910	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56174047	0.86[EUR][1000 genomes]
rs56279747	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56289966	0.83[EUR][1000 genomes]
rs56333123	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56393662	0.98[ASN][1000 genomes]
rs62326764	0.83[EUR][1000 genomes]
rs62326797	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62326801	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62326802	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62326804	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62326848	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6537399	0.83[EUR][1000 genomes]
rs6537400	0.84[EUR][1000 genomes]
rs6537401	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6537402	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6537403	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6813969	0.85[CEU][hapmap]
rs6815527	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6816161	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6820462	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821066	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821444	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821479	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821863	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6824313	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6832576	0.84[EUR][1000 genomes]
rs6838174	0.88[CEU][hapmap]
rs6838458	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6839123	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6839141	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6843421	0.85[CEU][hapmap]
rs6844381	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6856647	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6858813	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72727922	0.83[EUR][1000 genomes]
rs72727944	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72727952	0.98[ASN][1000 genomes]
rs7657269	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7665079	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7695415	0.84[EUR][1000 genomes]
rs7745	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs919482	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs919483	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9308199	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461674	chr4:147047072-147143572	Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv595650	chr4:147047072-147143572	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1018859	chr4:147055618-147138397	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs17757522	RP11-6L6.2	cis	Nerve Tibial	GTEx
rs17757522	HHIP	cis	cerebellum	SCAN
rs17757522	LSM6	cis	parietal	SCAN
rs17757522	RP11-6L6.2	cis	Adipose Subcutaneous	GTEx
rs17757522	LSM6	cis	cerebellum	SCAN
rs17757522	RP11-6L6.2	cis	Whole Blood	GTEx
rs17757522	RP11-6L6.2	cis	Skin Sun Exposed Lower leg	GTEx
rs17757522	RP11-6L6.2	cis	lung	GTEx
rs17757522	RP11-6L6.2	cis	Artery Tibial	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:147097600-147108800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:147097800-147104200	Weak transcription	Placenta	Placenta
3	chr4:147097800-147104600	Weak transcription	Fetal Muscle Trunk	muscle
4	chr4:147097800-147108600	Weak transcription	HSMMtube	muscle
5	chr4:147097800-147108800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:147097800-147108800	Weak transcription	Esophagus	oesophagus
7	chr4:147097800-147111000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr4:147097800-147115400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr4:147098400-147104200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr4:147098400-147104400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr4:147098400-147107400	Weak transcription	HSMM	muscle
12	chr4:147098400-147107800	Weak transcription	Fetal Kidney	kidney
13	chr4:147098400-147108000	Weak transcription	NH-A	brain
14	chr4:147098400-147108800	Weak transcription	NHLF	lung
15	chr4:147098400-147111400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr4:147098400-147118600	Weak transcription	Colonic Mucosa	Colon
17	chr4:147098600-147103800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr4:147098600-147103800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr4:147098600-147104000	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr4:147098600-147104200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr4:147098600-147104200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr4:147098600-147104400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr4:147098600-147105800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr4:147098600-147107800	Weak transcription	HMEC	breast
25	chr4:147098600-147113800	Weak transcription	Hela-S3	cervix
26	chr4:147099000-147104400	Weak transcription	Fetal Intestine Large	intestine
27	chr4:147099000-147108400	Weak transcription	Aorta	Aorta
28	chr4:147099200-147107400	Weak transcription	Osteobl	bone
29	chr4:147099200-147107600	Weak transcription	Brain Germinal Matrix	brain
30	chr4:147099400-147104200	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr4:147099400-147104200	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr4:147099400-147107800	Weak transcription	Thymus	Thymus
33	chr4:147099400-147108000	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr4:147099400-147108200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr4:147099400-147109400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr4:147099600-147103800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr4:147099600-147104400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr4:147099800-147104200	Weak transcription	Fetal Thymus	thymus
39	chr4:147100000-147103800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr4:147100000-147103800	Weak transcription	Primary B cells from cord blood	blood
41	chr4:147100000-147107800	Weak transcription	Brain Cingulate Gyrus	brain
42	chr4:147100200-147107800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr4:147100200-147108800	Weak transcription	Fetal Stomach	stomach
44	chr4:147100200-147108800	Weak transcription	HUVEC	blood vessel
45	chr4:147101000-147105000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr4:147101200-147103800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr4:147101200-147103800	Weak transcription	Primary T cells from cord blood	blood
48	chr4:147101200-147104400	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr4:147101200-147104400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr4:147101200-147108200	Weak transcription	H9 Cell Line	embryonic stem cell

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