Variant report

Variant	rs4715631
Chromosome Location	chr6:56417545-56417546
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56406262..56407921-chr6:56416925..56419390,3	K562	blood:
2	chr6:56406220..56410337-chr6:56413126..56418049,5	MCF-7	breast:
3	chr6:56408981..56412253-chr6:56415239..56417908,3	K562	blood:
4	chr6:56416932..56418493-chr6:56421401..56422998,2	MCF-7	breast:
5	chr6:56413498..56416394-chr6:56417084..56419483,2	K562	blood:

Variant related genes	Relation type
ENSG00000151914	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs11753813	0.91[CEU][hapmap];0.93[GIH][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes]
rs11756977	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11758339	0.86[GIH][hapmap];0.83[MEX][hapmap]
rs11759493	0.89[GIH][hapmap];0.83[MEX][hapmap]
rs12527139	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13194746	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13219448	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1535610	0.81[EUR][1000 genomes]
rs1535612	0.91[CEU][hapmap];0.93[GIH][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes]
rs16887974	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17825773	0.84[MEX][hapmap]
rs2064591	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2273972	0.86[GIH][hapmap];0.84[MEX][hapmap]
rs2273973	0.91[CEU][hapmap];0.93[GIH][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap]
rs4130060	0.80[AMR][1000 genomes]
rs4143827	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4143828	0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4236139	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4236140	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4236141	0.91[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4236142	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4236143	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4236144	0.81[CEU][hapmap];0.81[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4236145	0.98[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4283892	0.89[GIH][hapmap];0.83[MEX][hapmap]
rs4329120	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4346846	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4454141	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4466244	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4472350	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4473850	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4499917	0.89[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes]
rs4712132	0.83[ASW][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4712133	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4715626	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4715627	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4715628	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4715629	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4715630	0.95[GIH][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6459161	0.81[CEU][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap]
rs6904202	0.91[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6906792	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6907917	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6911502	0.82[GIH][hapmap];0.83[MEX][hapmap]
rs6914184	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6919608	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6922770	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6939305	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71549713	0.80[AMR][1000 genomes]
rs721475	0.81[EUR][1000 genomes]
rs7741295	0.89[GIH][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes]
rs7743011	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7755361	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7755573	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7758054	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7759875	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7760640	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7760695	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7761281	0.94[ASW][hapmap];0.86[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7762629	0.86[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9296848	0.89[GIH][hapmap];0.83[MEX][hapmap]
rs9296849	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9296850	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9349826	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9357921	0.91[CEU][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9357922	0.85[CEU][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9370533	0.84[CEU][hapmap]
rs9396213	0.91[GIH][hapmap];0.83[MEX][hapmap]
rs9396214	0.89[GIH][hapmap];0.83[MEX][hapmap]
rs9396218	0.81[EUR][1000 genomes]
rs9396220	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9464389	0.80[AMR][1000 genomes]
rs9475709	0.81[EUR][1000 genomes]
rs9475713	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9475714	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830666	chr6:56243743-56419599	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv885912	chr6:56327849-56458836	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1016868	chr6:56376165-56417631	Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
5	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4715631	DST	cis	cerebellum	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56408200-56419400	Weak transcription	Placenta	Placenta
2	chr6:56408200-56419800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr6:56408200-56440400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:56408200-56440600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:56408200-56496000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr6:56408400-56430800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr6:56411800-56419600	Weak transcription	A549	lung
8	chr6:56412000-56417600	Enhancers	Brain Anterior Caudate	brain
9	chr6:56412800-56418000	Enhancers	Rectal Smooth Muscle	rectum
10	chr6:56413200-56419600	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr6:56413600-56417600	Enhancers	Brain Hippocampus Middle	brain
12	chr6:56413800-56458400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr6:56414000-56419600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr6:56414400-56418000	Genic enhancers	HSMM	muscle
15	chr6:56415200-56418400	Genic enhancers	HSMMtube	muscle
16	chr6:56415400-56417600	Genic enhancers	Muscle Satellite Cultured Cells	--
17	chr6:56415400-56427000	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr6:56415600-56417800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr6:56415600-56417800	Genic enhancers	Fetal Intestine Large	intestine
20	chr6:56415600-56418400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr6:56415800-56418200	Genic enhancers	NHDF-Ad	bronchial
22	chr6:56415800-56418400	Genic enhancers	Osteobl	bone
23	chr6:56415800-56418800	Enhancers	Colon Smooth Muscle	Colon
24	chr6:56415800-56419800	Weak transcription	NHEK	skin
25	chr6:56415800-56426000	Weak transcription	Ovary	ovary
26	chr6:56415800-56435200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr6:56416000-56419600	Weak transcription	Fetal Heart	heart
28	chr6:56416000-56420200	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr6:56416000-56421000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr6:56416200-56418600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr6:56416200-56418600	Strong transcription	Fetal Lung	lung
32	chr6:56416200-56418800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr6:56416200-56418800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr6:56416200-56419800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:56416200-56420800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr6:56416200-56423000	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr6:56416400-56417600	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr6:56416400-56417600	Genic enhancers	Placenta Amnion	Placenta Amnion
39	chr6:56416400-56418400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr6:56416400-56424200	Strong transcription	GM12878-XiMat	blood
41	chr6:56416400-56426800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr6:56416400-56427000	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr6:56416600-56417600	Genic enhancers	Left Ventricle	heart
44	chr6:56416600-56417800	Genic enhancers	NHLF	lung
45	chr6:56416600-56418400	Genic enhancers	NH-A	brain
46	chr6:56416800-56417600	Genic enhancers	Liver	Liver
47	chr6:56416800-56417800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr6:56416800-56417800	Strong transcription	Brain Germinal Matrix	brain
49	chr6:56416800-56417800	Strong transcription	Fetal Muscle Trunk	muscle
50	chr6:56416800-56417800	Strong transcription	Fetal Stomach	stomach

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