Variant report

Variant	rs41701
Chromosome Location	chr7:120640410-120640411
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:120590021..120592843-chr7:120639404..120643575,5	K562	blood:
2	chr7:120621518..120649031-chr7:120712706..120728931,108	K562	blood:
3	chr7:120624020..120645873-chr7:120713358..120727138,77	K562	blood:

Variant related genes	Relation type
ENSG00000212628	Chromatin interaction
ENSG00000106034	Chromatin interaction
ENSG00000071243	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10245811	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11976117	0.90[CEU][hapmap];0.85[CHB][hapmap];0.87[JPT][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12666371	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12671499	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12673175	0.94[AFR][1000 genomes]
rs16870531	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41696	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41699	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4730984	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62470917	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7782014	0.89[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.83[TSI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7802570	0.85[CHB][hapmap];0.87[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7802665	0.88[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.88[TSI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831114	chr7:120595624-120804510	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv608327	chr7:120633006-120873078	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv2753621	chr7:120635049-120800049	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1030988	chr7:120636796-120672504	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1023611	chr7:120638930-120881658	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41701	FLJ21986	cis	multi-tissue	Pritchard

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120632400-120641400	Transcr. at gene 5' and 3'	K562	blood
2	chr7:120634200-120644000	Weak transcription	Spleen	Spleen
3	chr7:120635000-120640800	Enhancers	Dnd41	blood
4	chr7:120636200-120640800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr7:120636400-120640600	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr7:120637000-120641000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr7:120637000-120641400	Weak transcription	Fetal Muscle Leg	muscle
8	chr7:120637000-120642000	Weak transcription	Brain Hippocampus Middle	brain
9	chr7:120637000-120646800	Weak transcription	Placenta	Placenta
10	chr7:120637200-120640800	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr7:120637200-120640800	Weak transcription	Small Intestine	intestine
12	chr7:120637200-120641800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr7:120637200-120647000	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr7:120637200-120663600	Weak transcription	Right Ventricle	heart
15	chr7:120637400-120642200	Weak transcription	Fetal Heart	heart
16	chr7:120637800-120640800	Enhancers	Fetal Kidney	kidney
17	chr7:120638200-120643600	Weak transcription	Left Ventricle	heart
18	chr7:120638800-120640600	Active TSS	Aorta	Aorta
19	chr7:120638800-120643800	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr7:120639000-120645000	Enhancers	Liver	Liver
21	chr7:120639400-120641600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr7:120639600-120640600	Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr7:120639600-120641000	Enhancers	Fetal Lung	lung
24	chr7:120639800-120640600	Active TSS	Colon Smooth Muscle	Colon
25	chr7:120639800-120640600	Active TSS	Stomach Smooth Muscle	stomach
26	chr7:120639800-120640600	Active TSS	NHLF	lung
27	chr7:120639800-120640800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr7:120639800-120640800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr7:120640000-120640600	Active TSS	Right Atrium	heart
30	chr7:120640000-120640600	Active TSS	NHDF-Ad	bronchial
31	chr7:120640000-120640600	Flanking Active TSS	Osteobl	bone
32	chr7:120640000-120640800	Enhancers	HSMMtube	muscle
33	chr7:120640000-120644800	Enhancers	Fetal Stomach	stomach
34	chr7:120640200-120640600	Active TSS	Ovary	ovary
35	chr7:120640200-120640800	Active TSS	NH-A	brain
36	chr7:120640400-120640600	Enhancers	Primary hematopoietic stem cells	blood
37	chr7:120640400-120640600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr7:120640400-120640600	Enhancers	Adipose Nuclei	Adipose
39	chr7:120640400-120640600	Flanking Active TSS	Rectal Smooth Muscle	rectum
40	chr7:120640400-120640800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr7:120640400-120640800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr7:120640400-120640800	Enhancers	Brain Anterior Caudate	brain
43	chr7:120640400-120640800	Enhancers	Psoas Muscle	Psoas
44	chr7:120640400-120641400	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr7:120640400-120641400	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr7:120640400-120642000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr7:120640400-120642000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr7:120640400-120642200	Enhancers	Muscle Satellite Cultured Cells	--
49	chr7:120640400-120642200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr7:120640400-120642200	Weak transcription	Hela-S3	cervix

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