Variant report

Variant	rs3735617
Chromosome Location	chr7:19735766-19735767
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:19733366..19735226-chr7:19735376..19737263,2	K562	blood:
2	chr7:19733161..19736088-chr7:19743842..19746226,2	K562	blood:
3	chr7:19733619..19736349-chr7:19737994..19740967,3	K562	blood:
4	chr7:19727945..19730939-chr7:19734576..19737484,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000265932	Chromatin interaction
ENSG00000105849	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12532153	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12536065	0.87[AMR][1000 genomes]
rs12667746	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4591920	0.86[AMR][1000 genomes]
rs4620176	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59113291	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61223965	0.89[EUR][1000 genomes]
rs67120244	0.87[AMR][1000 genomes]
rs67568939	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67733453	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6962595	0.90[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72591424	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72591425	0.81[ASN][1000 genomes]
rs73274023	0.82[AFR][1000 genomes]
rs7803245	0.81[ASN][1000 genomes]
rs9690344	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs992934	0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018601	chr7:19272360-20008881	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1033223	chr7:19682192-20461375	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv538795	chr7:19682192-20461375	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv524807	chr7:19714156-19803925	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3735617	AGR3	cis	parietal	SCAN
rs3735617	SNX13	cis	parietal	SCAN
rs3735617	MACC1	cis	cerebellum	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:19729400-19737000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr7:19729400-19739800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr7:19729600-19736000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:19729800-19737000	Weak transcription	K562	blood
5	chr7:19729800-19745000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr7:19730400-19736600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr7:19730400-19738000	Weak transcription	Left Ventricle	heart
8	chr7:19730400-19747400	Weak transcription	HSMMtube	muscle
9	chr7:19730600-19736600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr7:19730600-19736800	Weak transcription	Hela-S3	cervix
11	chr7:19731000-19736800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr7:19731000-19746000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr7:19731600-19746400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr7:19732200-19743400	Weak transcription	Esophagus	oesophagus
15	chr7:19732400-19737600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr7:19732400-19737600	Weak transcription	Placenta	Placenta
17	chr7:19732400-19745400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr7:19732600-19736400	Weak transcription	Fetal Thymus	thymus
19	chr7:19732600-19736600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr7:19732600-19737000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr7:19732600-19747000	Weak transcription	Pancreas	Pancrea
22	chr7:19733000-19745600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr7:19733000-19747400	Weak transcription	Spleen	Spleen
24	chr7:19733200-19736400	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr7:19733200-19736600	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr7:19733200-19737600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr7:19733400-19736600	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr7:19733600-19736600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr7:19733600-19736800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr7:19733800-19747000	Weak transcription	Osteobl	bone
31	chr7:19733800-19747400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr7:19734000-19735800	Weak transcription	Primary B cells from peripheral blood	blood
33	chr7:19734000-19736600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr7:19734000-19736600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr7:19734000-19736800	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr7:19734000-19736800	Weak transcription	Primary B cells from cord blood	blood
37	chr7:19734000-19737000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr7:19734000-19737000	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr7:19734000-19737400	Weak transcription	HUVEC	blood vessel
40	chr7:19734000-19739600	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr7:19734000-19745600	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr7:19734000-19746000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr7:19734000-19746600	Weak transcription	Fetal Lung	lung
44	chr7:19734200-19736600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr7:19734200-19736600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr7:19734200-19736600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr7:19734200-19736600	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr7:19734200-19737000	Weak transcription	GM12878-XiMat	blood
49	chr7:19734200-19737600	Weak transcription	Brain Germinal Matrix	brain
50	chr7:19734200-19739400	Weak transcription	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links