Variant report

Variant	rs3801382
Chromosome Location	chr7:120998277-120998278
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:120945110..120947214-chr7:120997480..120999787,2	K562	blood:
2	chr7:120995819..120998464-chr7:121018904..121020746,2	K562	blood:
3	chr7:120996529..120999253-chr7:121021354..121023479,2	K562	blood:
4	chr7:120998130..121000230-chr7:121033883..121036363,2	MCF-7	breast:
5	chr7:120991538..120993968-chr7:120997177..121000035,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196937	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10242100	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12171617	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12531355	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12539772	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2536182	1.00[CHB][hapmap];0.97[ASN][1000 genomes]
rs28395249	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3779381	1.00[CHB][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3801383	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3801387	0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55963900	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56364616	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs718766	0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7776725	0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7801915	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7807953	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7808155	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs917726	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs917727	0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025430	chr7:120638930-121179289	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1034353	chr7:120818382-121040576	Enhancers Bivalent Enhancer Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1026322	chr7:120841937-121188037	Weak transcription Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv539102	chr7:120841937-121188037	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	esv2755350	chr7:120848049-121119049	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv1032054	chr7:120926379-121432971	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv539103	chr7:120926379-121432971	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	esv1799806	chr7:120997195-121008204	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3801382	FAM3C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120970600-121016800	Weak transcription	Gastric	stomach
2	chr7:120970600-121025400	Weak transcription	Spleen	Spleen
3	chr7:120970800-121000400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr7:120973800-120998800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr7:120977800-120999800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr7:120978800-121017400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr7:120979800-121019400	Weak transcription	Thymus	Thymus
8	chr7:120979800-121034800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr7:120980800-121019600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr7:120981000-121015200	Weak transcription	Pancreas	Pancrea
11	chr7:120983000-121009600	Weak transcription	Hela-S3	cervix
12	chr7:120983800-121000200	Weak transcription	Fetal Kidney	kidney
13	chr7:120984000-121017600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr7:120984200-121001200	Weak transcription	NHLF	lung
15	chr7:120984200-121009800	Weak transcription	Fetal Brain Male	brain
16	chr7:120984200-121035000	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr7:120984800-121009600	Weak transcription	A549	lung
18	chr7:120985000-121001200	Weak transcription	Brain Hippocampus Middle	brain
19	chr7:120985000-121009600	Weak transcription	Small Intestine	intestine
20	chr7:120985200-121000000	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr7:120985200-121013000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr7:120986200-121029600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr7:120986400-121026000	Weak transcription	Colonic Mucosa	Colon
24	chr7:120986400-121026000	Weak transcription	Psoas Muscle	Psoas
25	chr7:120987600-121003800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr7:120989200-120999000	Weak transcription	HepG2	liver
27	chr7:120989200-121015400	Weak transcription	Brain Anterior Caudate	brain
28	chr7:120989600-121016800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr7:120990400-120998800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr7:120990400-121002400	Strong transcription	NH-A	brain
31	chr7:120990400-121005000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr7:120990400-121005200	Strong transcription	Dnd41	blood
33	chr7:120990400-121006000	Strong transcription	Primary B cells from peripheral blood	blood
34	chr7:120990400-121006200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr7:120990400-121007000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr7:120990400-121008600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr7:120990600-120998800	Strong transcription	Osteobl	bone
38	chr7:120990600-121000000	Strong transcription	NHDF-Ad	bronchial
39	chr7:120990600-121004200	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr7:120990600-121004800	Strong transcription	Muscle Satellite Cultured Cells	--
41	chr7:120990600-121005000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr7:120990600-121006600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr7:120990600-121008800	Strong transcription	Duodenum Mucosa	Duodenum
44	chr7:120990600-121009000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr7:120990600-121009000	Strong transcription	HSMM	muscle
46	chr7:120991000-121012600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr7:120991200-121005200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr7:120991800-121010800	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr7:120992400-120998600	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr7:120992400-120998600	Strong transcription	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links