Variant report

Variant	rs4722006
Chromosome Location	chr7:2765723-2765724
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:2763542..2765998-chr7:2913273..2914846,2	MCF-7	breast:
2	chr7:2760749..2763045-chr7:2764793..2766522,2	K562	blood:
3	chr7:2758129..2761976-chr7:2763173..2766287,3	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10480003	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11354	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1182190	0.82[MKK][hapmap]
rs12484	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17339470	0.80[CHB][hapmap]
rs2266922	0.83[YRI][hapmap]
rs2527686	0.81[LWK][hapmap]
rs4719646	0.81[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap]
rs4719647	0.83[ASN][1000 genomes]
rs4719648	0.81[ASN][1000 genomes]
rs4719654	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4722008	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6461550	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6944607	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6965989	0.83[ASN][1000 genomes]
rs709282	0.92[AFR][1000 genomes]
rs757791	0.84[MKK][hapmap]
rs7797295	0.81[ASN][1000 genomes]
rs7805092	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7807978	0.82[MKK][hapmap]
rs798492	0.87[YRI][hapmap]
rs798499	1.00[YRI][hapmap]
rs798503	0.84[LWK][hapmap];0.89[MKK][hapmap];0.81[YRI][hapmap]
rs798512	1.00[YRI][hapmap]
rs798531	0.92[AFR][1000 genomes]
rs9332401	0.80[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471227	chr7:2629020-2768864	Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv1029250	chr7:2722737-2881021	Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv538652	chr7:2722737-2881021	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1024023	chr7:2726210-2829581	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv538653	chr7:2726210-2829581	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1017611	chr7:2750418-2781716	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv538654	chr7:2750418-2781716	Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1015700	chr7:2753965-2945848	Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
9	nsv971480	chr7:2755767-2765866	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4722006	IQCE	cis	cerebellum	SCAN
rs4722006	RPN2	trans	parietal	SCAN
rs4722006	LOC392620	cis	multi-tissue	Pritchard
rs4722006	GNA12	cis	Nerve Tibial	GTEx
rs4722006		cis	Lymphoblastoid	GTEx
rs4722006	GNA12	cis	lymphoblastoid	seeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:2749400-2770600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr7:2749800-2770800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:2750000-2767800	Weak transcription	Osteobl	bone
4	chr7:2750000-2768400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr7:2750000-2769000	Weak transcription	NHDF-Ad	bronchial
6	chr7:2750200-2765800	Weak transcription	Liver	Liver
7	chr7:2751200-2768400	Weak transcription	Brain Angular Gyrus	brain
8	chr7:2752400-2796000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr7:2753400-2765800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr7:2753600-2768800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr7:2754600-2766800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr7:2754800-2774200	Weak transcription	Fetal Brain Male	brain
13	chr7:2755800-2770600	Weak transcription	Fetal Kidney	kidney
14	chr7:2756000-2777800	Weak transcription	Psoas Muscle	Psoas
15	chr7:2756200-2770600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr7:2757200-2767400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr7:2757200-2770600	Weak transcription	Esophagus	oesophagus
18	chr7:2757400-2766200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr7:2757600-2772800	Weak transcription	Small Intestine	intestine
20	chr7:2757800-2766800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr7:2757800-2768200	Weak transcription	Colon Smooth Muscle	Colon
22	chr7:2757800-2768400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr7:2758000-2765800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr7:2758000-2768400	Weak transcription	HepG2	liver
25	chr7:2758000-2768600	Weak transcription	Right Atrium	heart
26	chr7:2758200-2766000	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr7:2758200-2768000	Strong transcription	Fetal Stomach	stomach
28	chr7:2758200-2769400	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr7:2758400-2765800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr7:2758600-2765800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr7:2758600-2765800	Weak transcription	Duodenum Mucosa	Duodenum
32	chr7:2758600-2767200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr7:2758600-2769400	Strong transcription	Fetal Intestine Small	intestine
34	chr7:2758600-2769800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr7:2758600-2771600	Weak transcription	K562	blood
36	chr7:2758800-2765800	Weak transcription	Primary T cells from cord blood	blood
37	chr7:2759000-2768200	Weak transcription	Brain Anterior Caudate	brain
38	chr7:2759200-2774000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr7:2759400-2766600	Strong transcription	Stomach Smooth Muscle	stomach
40	chr7:2759400-2771600	Strong transcription	Pancreas	Pancrea
41	chr7:2759600-2766600	Strong transcription	NHLF	lung
42	chr7:2760600-2767200	Weak transcription	Primary hematopoietic stem cells	blood
43	chr7:2760600-2767200	Strong transcription	Lung	lung
44	chr7:2760800-2766000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr7:2760800-2770200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr7:2761000-2765800	Weak transcription	HMEC	breast
47	chr7:2761000-2765800	Weak transcription	NHEK	skin
48	chr7:2761000-2766000	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr7:2761000-2766000	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr7:2761000-2767200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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