Variant report

Variant	rs6702344
Chromosome Location	chr1:151092086-151092087
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:151091415..151093045-chr1:151095396..151097246,2	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10788800	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs10888405	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11204772	0.82[EUR][1000 genomes]
rs4357530	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4360524	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs61819219	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6656450	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6676190	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7536234	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
5	nsv872421	chr1:151055670-151098077	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6702344	BNIPL	cis	lung	GTEx
rs6702344	LYSMD1	Cis_1M	lymphoblastoid	RTeQTL
rs6702344	CDC42SE1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151044400-151103600	Weak transcription	Small Intestine	intestine
2	chr1:151044800-151098800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr1:151052200-151103000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:151061800-151105600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr1:151064200-151103400	Weak transcription	Colonic Mucosa	Colon
6	chr1:151067000-151103400	Weak transcription	Fetal Brain Male	brain
7	chr1:151074000-151101000	Weak transcription	Fetal Heart	heart
8	chr1:151078000-151096400	Strong transcription	Fetal Intestine Small	intestine
9	chr1:151079200-151093800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:151079600-151096400	Weak transcription	Hela-S3	cervix
11	chr1:151079800-151097000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:151079800-151102000	Weak transcription	NHDF-Ad	bronchial
13	chr1:151079800-151103400	Weak transcription	NH-A	brain
14	chr1:151079800-151103400	Weak transcription	NHEK	skin
15	chr1:151079800-151103400	Weak transcription	NHLF	lung
16	chr1:151079800-151106200	Weak transcription	HSMMtube	muscle
17	chr1:151079800-151114800	Weak transcription	HSMM	muscle
18	chr1:151081000-151100800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr1:151081200-151095000	Weak transcription	Aorta	Aorta
20	chr1:151081200-151102000	Weak transcription	Brain Germinal Matrix	brain
21	chr1:151081200-151103400	Weak transcription	GM12878-XiMat	blood
22	chr1:151081400-151103000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr1:151081600-151097000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr1:151081800-151097400	Weak transcription	Stomach Mucosa	stomach
25	chr1:151081800-151103000	Weak transcription	Colon Smooth Muscle	Colon
26	chr1:151083400-151103600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:151085000-151092600	Strong transcription	Fetal Thymus	thymus
28	chr1:151085000-151093800	Strong transcription	Thymus	Thymus
29	chr1:151085800-151103200	Weak transcription	Fetal Muscle Leg	muscle
30	chr1:151086400-151093000	Strong transcription	Fetal Stomach	stomach
31	chr1:151087000-151103600	Weak transcription	Psoas Muscle	Psoas
32	chr1:151088200-151097200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr1:151088400-151095200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr1:151089000-151095400	Weak transcription	Primary hematopoietic stem cells	blood
35	chr1:151089200-151098000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr1:151089200-151103600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr1:151089600-151093000	Strong transcription	Brain Inferior Temporal Lobe	brain
38	chr1:151089800-151092200	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr1:151089800-151092200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr1:151089800-151092200	Strong transcription	Brain Cingulate Gyrus	brain
41	chr1:151090000-151092800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr1:151090200-151093800	Strong transcription	Brain Anterior Caudate	brain
43	chr1:151090200-151095000	Strong transcription	Liver	Liver
44	chr1:151090200-151095400	Strong transcription	Brain Hippocampus Middle	brain
45	chr1:151090400-151092800	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr1:151090800-151095200	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr1:151090800-151097000	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr1:151090800-151102000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr1:151090800-151103200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr1:151090800-151103400	Weak transcription	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links