Variant report

Variant	rs4700397
Chromosome Location	chr5:60135962-60135963
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1021005	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10805374	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10939879	0.86[ASN][1000 genomes]
rs11739952	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11740632	0.82[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12516995	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12517310	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12652830	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12652878	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12654306	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12655209	0.80[EUR][1000 genomes]
rs12655603	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1382917	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1471488	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1479645	0.86[ASN][1000 genomes]
rs17332824	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17392014	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17419290	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1807017	0.81[CEU][hapmap];0.92[CHB][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2120956	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2120957	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28436304	0.85[ASN][1000 genomes]
rs2898309	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34741733	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797559	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4642318	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4647052	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4647132	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4647137	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4647150	0.85[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4700399	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4700402	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4700404	0.85[ASN][1000 genomes]
rs55738840	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55814394	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56031340	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56350217	0.82[EUR][1000 genomes]
rs58078456	0.93[ASN][1000 genomes]
rs58646987	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60858663	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61017995	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61101592	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62365455	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62365458	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62367862	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62367872	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62367878	0.81[EUR][1000 genomes]
rs62367879	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62367885	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62367903	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62372102	0.89[ASN][1000 genomes]
rs62372103	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62372133	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62372134	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6449512	0.83[EUR][1000 genomes]
rs67490467	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67555188	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67858932	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6884966	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs726824	0.85[ASN][1000 genomes]
rs72757187	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72759206	0.85[ASN][1000 genomes]
rs7701398	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7709522	0.84[ASN][1000 genomes]
rs7722373	1.00[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7723349	0.85[ASN][1000 genomes]
rs7723901	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs868791	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9687099	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs976630	0.92[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs976631	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492277	chr5:59905195-60180834	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv934153	chr5:60004982-60309751	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	esv2763456	chr5:60007355-60151767	Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv1026190	chr5:60020156-60148535	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv537769	chr5:60020156-60148535	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
6	esv2752073	chr5:60034475-60136626	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
7	nsv949662	chr5:60047974-60488379	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
8	nsv1017095	chr5:60050600-60414783	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv933326	chr5:60074031-60413061	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
10	nsv881712	chr5:60116613-60266875	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv881713	chr5:60116613-60305125	Strong transcription Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv598305	chr5:60116613-60308836	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	nsv881714	chr5:60116613-60313015	Bivalent Enhancer Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
14	nsv881715	chr5:60116613-60356423	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
15	nsv598306	chr5:60129361-60266875	Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
16	nsv598307	chr5:60129361-60308836	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
17	nsv881716	chr5:60129361-60313015	Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
18	nsv462199	chr5:60129361-60329624	Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
19	nsv598308	chr5:60129361-60329624	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4700397	mimitin	cis	multi-tissue	Pritchard
rs4700397	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL
rs4700397	ERCC8	Cis_1M	lymphoblastoid	RTeQTL
rs4700397	DEPDC1B	cis	cerebellum	SCAN
rs4700397	KIF2A	cis	parietal	SCAN
rs4700397	ERCC8	cis	multi-tissue	Pritchard
rs4700397	ELOVL7	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60102200-60137800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr5:60129400-60137200	Weak transcription	Fetal Intestine Small	intestine
3	chr5:60132000-60138600	Weak transcription	HMEC	breast
4	chr5:60132400-60138600	Weak transcription	A549	lung
5	chr5:60134200-60137200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:60134200-60137400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr5:60134400-60138000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr5:60134400-60138400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr5:60134400-60138400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr5:60134400-60138400	Weak transcription	Gastric	stomach
11	chr5:60134400-60138400	Weak transcription	Pancreas	Pancrea
12	chr5:60134400-60138400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr5:60134400-60139000	Weak transcription	Lung	lung
14	chr5:60134400-60139000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr5:60134600-60137000	Weak transcription	Fetal Intestine Large	intestine
16	chr5:60135400-60136200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr5:60135400-60136400	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr5:60135600-60136400	Active TSS	Brain Anterior Caudate	brain
19	chr5:60135600-60136600	Enhancers	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links