Variant report

Variant	rs11239961
Chromosome Location	chr1:146734115-146734116
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:146728735..146731068-chr1:146731372..146734361,2	MCF-7	breast:
2	chr1:146724955..146727142-chr1:146731983..146734625,2	MCF-7	breast:
3	chr1:146727066..146728885-chr1:146732769..146735404,3	K562	blood:
4	chr1:146732645..146734602-chr1:146737809..146740107,2	MCF-7	breast:
5	chr1:146727066..146728772-chr1:146732769..146735404,2	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11239954	0.86[YRI][hapmap];0.80[AFR][1000 genomes]
rs11239958	0.80[AFR][1000 genomes]
rs11239960	0.80[AFR][1000 genomes]
rs11800580	1.00[YRI][hapmap]
rs11802302	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12064458	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12066130	0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12070617	0.86[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12070655	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12078046	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17160050	0.86[YRI][hapmap];0.80[AFR][1000 genomes]
rs17160051	0.85[YRI][hapmap];0.80[AFR][1000 genomes]
rs17160059	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs72691016	0.80[AFR][1000 genomes]
rs72691025	0.80[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872251	chr1:146152553-146803630	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv872252	chr1:146471863-147398135	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
3	nsv999546	chr1:146507577-147356574	Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
4	nsv535123	chr1:146507577-147356574	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
5	nsv492188	chr1:146507649-147381479	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
6	nsv916754	chr1:146507711-147417736	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	113 gene(s)	inside rSNPs	diseases
7	nsv547673	chr1:146510112-147398135	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
8	nsv547674	chr1:146522722-147396797	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
9	nsv998341	chr1:146531446-147384720	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats 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	110 gene(s)	inside rSNPs	diseases
10	nsv535124	chr1:146531446-147384720	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
11	nsv1003493	chr1:146531446-147389944	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
12	nsv998209	chr1:146543722-147384720	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
13	nsv535126	chr1:146543722-147384720	Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
14	nsv872255	chr1:146550780-146969712	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
15	nsv872256	chr1:146556596-147410973	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
16	nsv1012331	chr1:146603479-147384720	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
17	nsv535131	chr1:146603479-147384720	Genic enhancers Strong transcription Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
18	nsv1009943	chr1:146618929-146893851	Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
19	nsv535132	chr1:146618929-146893851	Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
20	nsv437047	chr1:146643555-146841602	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
21	nsv1005809	chr1:146647822-146886419	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
22	nsv535134	chr1:146647822-146886419	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
23	nsv1004849	chr1:146661516-147286826	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
24	nsv535135	chr1:146661516-147286826	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
25	nsv547676	chr1:146686228-146996047	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:146715600-146736200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr1:146715600-146749400	Weak transcription	Colonic Mucosa	Colon
3	chr1:146715800-146756800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:146716000-146735600	Weak transcription	Ovary	ovary
5	chr1:146716000-146739600	Weak transcription	Colon Smooth Muscle	Colon
6	chr1:146716000-146743800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:146716800-146748600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr1:146717200-146751000	Weak transcription	Gastric	stomach
9	chr1:146717600-146736600	Weak transcription	Psoas Muscle	Psoas
10	chr1:146719400-146736400	Weak transcription	Brain Angular Gyrus	brain
11	chr1:146719400-146757600	Weak transcription	Stomach Mucosa	stomach
12	chr1:146719600-146736200	Weak transcription	Spleen	Spleen
13	chr1:146719600-146747600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:146719600-146747800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:146719600-146748000	Weak transcription	Small Intestine	intestine
16	chr1:146722200-146740200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr1:146722400-146740200	Weak transcription	Pancreas	Pancrea
18	chr1:146722600-146749400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:146722800-146769800	Strong transcription	Dnd41	blood
20	chr1:146723800-146761200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:146723800-146763200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr1:146724200-146739200	Weak transcription	Placenta	Placenta
23	chr1:146724200-146769800	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr1:146724400-146739400	Weak transcription	Brain Germinal Matrix	brain
25	chr1:146724600-146740200	Weak transcription	Esophagus	oesophagus
26	chr1:146725800-146735000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:146726000-146735200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:146726400-146735800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr1:146726600-146769600	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr1:146727000-146770000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr1:146727200-146734400	Strong transcription	A549	lung
32	chr1:146727200-146742000	Strong transcription	Liver	Liver
33	chr1:146727200-146744400	Strong transcription	Primary B cells from peripheral blood	blood
34	chr1:146727200-146754200	Strong transcription	Fetal Intestine Large	intestine
35	chr1:146727200-146762200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr1:146727200-146767800	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr1:146727200-146770200	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr1:146727400-146744400	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr1:146727400-146767800	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr1:146727400-146767800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr1:146727600-146743200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr1:146727600-146745000	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr1:146727800-146745400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr1:146728000-146735600	Weak transcription	NHDF-Ad	bronchial
45	chr1:146728200-146770800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr1:146728400-146736000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr1:146728600-146740200	Weak transcription	Rectal Smooth Muscle	rectum
48	chr1:146729200-146745200	Weak transcription	HSMMtube	muscle
49	chr1:146729400-146745000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr1:146729400-146769800	Strong transcription	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links