Variant report

Variant	rs4715630
Chromosome Location	chr6:56417282-56417283
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: 111 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs11751569	0.82[YRI][hapmap]
rs11753813	0.87[CEU][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap]
rs11756977	0.91[GIH][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11757910	0.80[YRI][hapmap]
rs11757941	0.82[YRI][hapmap]
rs11758339	1.00[ASW][hapmap];0.90[CEU][hapmap];0.87[CHB][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.87[LWK][hapmap];0.88[MEX][hapmap];0.91[YRI][hapmap]
rs11759493	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11961668	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12174955	0.90[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap]
rs12527139	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13194746	0.85[EUR][1000 genomes]
rs13204556	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13218268	0.82[YRI][hapmap]
rs13219448	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1359068	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1359070	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1535612	0.87[CEU][hapmap];0.87[CHB][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.81[ASN][1000 genomes]
rs16887974	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2064591	0.84[EUR][1000 genomes]
rs2273972	0.86[CEU][hapmap];0.91[GIH][hapmap]
rs2273973	0.87[CEU][hapmap];0.87[CHB][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap]
rs2273974	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2294697	0.82[YRI][hapmap]
rs2397221	1.00[ASW][hapmap];0.82[YRI][hapmap]
rs2397226	0.82[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.91[YRI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2894837	0.83[MEX][hapmap]
rs34954984	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35671304	0.82[EUR][1000 genomes]
rs35926142	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4130060	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[YRI][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4143827	0.83[EUR][1000 genomes]
rs4143828	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];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4236139	0.86[CEU][hapmap];0.89[GIH][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes]
rs4236140	1.00[CEU][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4236141	0.86[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4236142	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4236143	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4236144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4236145	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4283892	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4329120	0.83[EUR][1000 genomes]
rs4331988	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4346846	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs4454141	0.87[CEU][hapmap];0.87[GIH][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs4466244	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4472350	0.80[EUR][1000 genomes]
rs4473850	0.85[EUR][1000 genomes]
rs4499917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4544910	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs45486696	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4712132	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4712133	1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4715625	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4715626	0.87[CEU][hapmap];0.89[GIH][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs4715627	0.87[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs4715628	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs4715629	0.87[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs4715631	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]
rs595238	0.91[YRI][hapmap]
rs636389	1.00[ASW][hapmap];0.91[YRI][hapmap]
rs6459161	0.86[CEU][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap]
rs6459163	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6904202	0.86[CEU][hapmap];0.89[GIH][hapmap]
rs6906792	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs6907917	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6911502	1.00[ASW][hapmap];0.86[GIH][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.91[YRI][hapmap]
rs6913572	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6914184	0.82[EUR][1000 genomes]
rs6919608	0.89[GIH][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes]
rs6922770	0.87[CEU][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes]
rs6927258	0.86[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap]
rs6939305	0.90[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72877350	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7741295	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7743011	0.83[EUR][1000 genomes]
rs7746753	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7755361	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs7755573	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7758054	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7759875	0.89[CEU][hapmap];0.80[JPT][hapmap];0.86[EUR][1000 genomes]
rs7760640	0.86[CEU][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs7760695	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7761281	0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7762629	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7775847	0.82[YRI][hapmap]
rs9296848	0.87[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9296849	0.83[EUR][1000 genomes]
rs9296850	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9349823	0.89[CEU][hapmap];0.80[CHB][hapmap];0.80[JPT][hapmap]
rs9349825	0.82[AMR][1000 genomes]
rs9349826	0.83[EUR][1000 genomes]
rs9349828	0.93[JPT][hapmap]
rs9357921	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9357922	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9370533	0.90[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap]
rs9370534	0.90[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap]
rs9370535	1.00[CEU][hapmap];0.93[JPT][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9396213	0.82[CEU][hapmap];0.81[CHB][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap]
rs9396214	0.95[CEU][hapmap];0.87[CHB][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9396215	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9396220	0.84[EUR][1000 genomes]
rs9464389	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9475709	0.81[ASN][1000 genomes]
rs9475713	0.87[CEU][hapmap];0.89[GIH][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs9475714	0.87[CEU][hapmap];0.89[GIH][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs9475716	0.91[EUR][1000 genomes];0.92[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
rs4715630	ITGAX	trans	cerebellum	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56408200-56417400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr6:56408200-56419400	Weak transcription	Placenta	Placenta
3	chr6:56408200-56419800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr6:56408200-56440400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr6:56408200-56440600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr6:56408200-56496000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr6:56408400-56417400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:56408400-56417400	Weak transcription	HMEC	breast
9	chr6:56408400-56430800	Weak transcription	Primary hematopoietic stem cells	blood
10	chr6:56408600-56417400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:56411400-56417400	Enhancers	Brain Substantia Nigra	brain
12	chr6:56411800-56419600	Weak transcription	A549	lung
13	chr6:56412000-56417600	Enhancers	Brain Anterior Caudate	brain
14	chr6:56412800-56418000	Enhancers	Rectal Smooth Muscle	rectum
15	chr6:56413200-56419600	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr6:56413600-56417600	Enhancers	Brain Hippocampus Middle	brain
17	chr6:56413800-56458400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr6:56414000-56419600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr6:56414200-56417400	Weak transcription	HUVEC	blood vessel
20	chr6:56414400-56418000	Genic enhancers	HSMM	muscle
21	chr6:56415200-56418400	Genic enhancers	HSMMtube	muscle
22	chr6:56415400-56417600	Genic enhancers	Muscle Satellite Cultured Cells	--
23	chr6:56415400-56427000	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr6:56415600-56417400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr6:56415600-56417800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr6:56415600-56417800	Genic enhancers	Fetal Intestine Large	intestine
27	chr6:56415600-56418400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr6:56415800-56418200	Genic enhancers	NHDF-Ad	bronchial
29	chr6:56415800-56418400	Genic enhancers	Osteobl	bone
30	chr6:56415800-56418800	Enhancers	Colon Smooth Muscle	Colon
31	chr6:56415800-56419800	Weak transcription	NHEK	skin
32	chr6:56415800-56426000	Weak transcription	Ovary	ovary
33	chr6:56415800-56435200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr6:56416000-56417400	Enhancers	HepG2	liver
35	chr6:56416000-56419600	Weak transcription	Fetal Heart	heart
36	chr6:56416000-56420200	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr6:56416000-56421000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr6:56416200-56417400	Enhancers	Right Ventricle	heart
39	chr6:56416200-56418600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr6:56416200-56418600	Strong transcription	Fetal Lung	lung
41	chr6:56416200-56418800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr6:56416200-56418800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr6:56416200-56419800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr6:56416200-56420800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr6:56416200-56423000	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr6:56416400-56417400	Enhancers	Fetal Intestine Small	intestine
47	chr6:56416400-56417600	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr6:56416400-56417600	Genic enhancers	Placenta Amnion	Placenta Amnion
49	chr6:56416400-56418400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr6:56416400-56424200	Strong transcription	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links