Variant report

Variant	rs3800448
Chromosome Location	chr6:34885502-34885503
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:34852396..34857039-chr6:34885312..34888900,5	MCF-7	breast:
2	chr6:34879811..34884262-chr6:34884635..34888970,5	K562	blood:
3	chr6:34878922..34882866-chr6:34883896..34887915,4	MCF-7	breast:
4	chr6:34875439..34878531-chr6:34883509..34886060,3	MCF-7	breast:
5	chr6:34884853..34887138-chr6:34887416..34892086,4	K562	blood:

Variant related genes	Relation type
ENSG00000064995	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10947534	0.93[JPT][hapmap]
rs10947535	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs11755713	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs13204222	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13215944	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13220916	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16895035	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16895354	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1737724	0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1883639	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2030611	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2395601	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs34006431	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35057781	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35499928	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35760768	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35786848	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3734258	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs3734259	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3756859	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777750	0.88[JPT][hapmap]
rs3800443	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3800450	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800452	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800453	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3822923	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs4646919	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4646920	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4646922	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4646941	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56140217	0.85[ASN][1000 genomes]
rs57955553	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58595551	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6457799	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs6907427	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6912229	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6913108	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6918498	0.90[CHB][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs6927009	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6936820	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6941065	0.86[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs73745049	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73745050	1.00[ASN][1000 genomes]
rs7740148	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs7751820	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs7752468	0.93[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7755801	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7756122	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs847842	0.90[ASN][1000 genomes]
rs847844	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs847845	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs847861	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs847862	0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs861878	0.92[ASN][1000 genomes]
rs9357185	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9357187	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9366870	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9368835	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9368837	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9380465	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9380466	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9380467	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9380468	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9380470	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9380476	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs9394254	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9394255	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9394256	0.90[AFR][1000 genomes]
rs9784889	0.86[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022844	chr6:34317219-35060519	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv538195	chr6:34317219-35060519	Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv885793	chr6:34520267-34886436	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	esv2763967	chr6:34566255-34925463	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv1020710	chr6:34607214-34890143	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS 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	38 gene(s)	inside rSNPs	diseases
6	nsv1025374	chr6:34723723-34887316	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv462905	chr6:34728253-34886436	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	30 gene(s)	inside rSNPs	diseases
8	nsv602906	chr6:34728253-34886436	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	30 gene(s)	inside rSNPs	diseases
9	nsv1015792	chr6:34741917-34887316	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	30 gene(s)	inside rSNPs	diseases
10	nsv1021733	chr6:34751052-34887316	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	30 gene(s)	inside rSNPs	diseases
11	nsv1026121	chr6:34786887-34961360	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
12	nsv885797	chr6:34791027-34980601	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
13	nsv1033135	chr6:34802652-34957093	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
14	nsv508402	chr6:34840961-34951288	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34859200-34890800	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr6:34861600-34886000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr6:34869600-34890000	Weak transcription	Hela-S3	cervix
4	chr6:34871800-34886000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:34872400-34907200	Weak transcription	Small Intestine	intestine
6	chr6:34874400-34893200	Weak transcription	Fetal Intestine Large	intestine
7	chr6:34874800-34896000	Weak transcription	Brain Anterior Caudate	brain
8	chr6:34875600-34885800	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr6:34877000-34890000	Weak transcription	K562	blood
10	chr6:34877800-34892200	Weak transcription	Brain Angular Gyrus	brain
11	chr6:34877800-34921000	Weak transcription	Pancreas	Pancrea
12	chr6:34878000-34885600	Weak transcription	Fetal Heart	heart
13	chr6:34878000-34891400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr6:34878000-34896400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr6:34879600-34886000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr6:34879600-34892200	Weak transcription	Fetal Intestine Small	intestine
17	chr6:34879600-34892200	Weak transcription	Fetal Kidney	kidney
18	chr6:34879600-34893200	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr6:34879600-34896800	Weak transcription	Brain Hippocampus Middle	brain
20	chr6:34879800-34891800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr6:34879800-34893000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr6:34880000-34888800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:34880800-34893400	Weak transcription	Fetal Thymus	thymus
24	chr6:34881000-34889200	Weak transcription	Primary B cells from cord blood	blood
25	chr6:34881000-34898000	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr6:34881200-34887200	Weak transcription	NHEK	skin
27	chr6:34881200-34890200	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr6:34881200-34893000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr6:34881200-34928200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr6:34881400-34885800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:34881400-34887600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr6:34881400-34890000	Weak transcription	HMEC	breast
33	chr6:34881400-34896600	Weak transcription	Primary B cells from peripheral blood	blood
34	chr6:34881400-34902800	Weak transcription	Primary hematopoietic stem cells	blood
35	chr6:34881600-34887000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr6:34881600-34887200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr6:34881600-34890600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr6:34881600-34891800	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr6:34882600-34886000	Enhancers	Ovary	ovary
40	chr6:34882600-34886600	Enhancers	Right Atrium	heart
41	chr6:34882800-34885600	Weak transcription	HepG2	liver
42	chr6:34882800-34887200	Weak transcription	HSMM	muscle
43	chr6:34883200-34886800	Weak transcription	HUVEC	blood vessel
44	chr6:34883600-34886400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr6:34883800-34888000	Enhancers	Adipose Nuclei	Adipose
46	chr6:34884200-34885600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr6:34884200-34887200	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr6:34884400-34887400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr6:34884600-34885800	Enhancers	Fetal Muscle Leg	muscle
50	chr6:34884600-34886000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links