Variant report

Variant	rs11238519
Chromosome Location	chr10:43851825-43851826
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:43849709..43851969-chr10:43889837..43893145,4	MCF-7	breast:
2	chr10:43842333..43853034-chr10:43900806..43908178,21	MCF-7	breast:
3	chr10:43848751..43853953-chr10:43869065..43873618,8	MCF-7	breast:
4	chr10:43844277..43845840-chr10:43851755..43853493,2	MCF-7	breast:
5	chr10:43847403..43853479-chr10:43888233..43893881,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000150201	Chromatin interaction
ENSG00000169813	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11238518	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11238520	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11238531	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11238533	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11238547	1.00[ASN][1000 genomes]
rs11238570	1.00[ASN][1000 genomes]
rs12356024	1.00[ASN][1000 genomes]
rs12356570	1.00[ASN][1000 genomes]
rs12359520	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12359825	1.00[ASN][1000 genomes]
rs12359980	1.00[ASN][1000 genomes]
rs17366560	1.00[ASN][1000 genomes]
rs4646975	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4948720	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56120769	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56282135	0.80[AFR][1000 genomes]
rs60163354	1.00[ASN][1000 genomes]
rs61845676	1.00[ASN][1000 genomes]
rs61845680	1.00[ASN][1000 genomes]
rs61845682	1.00[ASN][1000 genomes]
rs61858993	1.00[ASN][1000 genomes]
rs61858995	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61859001	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61859441	1.00[ASN][1000 genomes]
rs61859445	1.00[ASN][1000 genomes]
rs61859998	1.00[ASN][1000 genomes]
rs61860007	1.00[ASN][1000 genomes]
rs61860889	1.00[ASN][1000 genomes]
rs67284218	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7073767	1.00[ASN][1000 genomes]
rs7079012	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7084706	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7093434	1.00[ASN][1000 genomes]
rs7100846	1.00[ASN][1000 genomes]
rs7900284	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7905073	1.00[ASN][1000 genomes]
rs7920408	0.80[AMR][1000 genomes];0.81[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	nsv430159	chr10:43291894-43946294	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv916378	chr10:43622151-43868356	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1043661	chr10:43626619-43890162	Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription 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	17 gene(s)	inside rSNPs	diseases
4	nsv540574	chr10:43626619-43890162	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1035873	chr10:43721143-43873664	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv1044422	chr10:43731521-43860307	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv895087	chr10:43783339-43982390	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
8	nsv831842	chr10:43846541-43987501	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43844400-43857200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr10:43846400-43852000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr10:43846600-43857200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr10:43848600-43852000	Enhancers	Brain Hippocampus Middle	brain
5	chr10:43848600-43852400	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr10:43849000-43857000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr10:43849200-43852000	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr10:43849200-43852400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr10:43849200-43852600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr10:43849400-43852400	Enhancers	NHEK	skin
11	chr10:43849400-43852600	Enhancers	K562	blood
12	chr10:43850000-43857000	Weak transcription	Brain Angular Gyrus	brain
13	chr10:43850000-43857000	Weak transcription	Brain Anterior Caudate	brain
14	chr10:43850000-43857000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr10:43850400-43852400	Enhancers	HMEC	breast
16	chr10:43850600-43852400	Weak transcription	Fetal Kidney	kidney
17	chr10:43850800-43852000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr10:43851200-43852000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr10:43851200-43852000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr10:43851200-43852000	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr10:43851200-43852000	Enhancers	Duodenum Mucosa	Duodenum
22	chr10:43851200-43852000	Enhancers	Rectal Mucosa Donor 29	rectum
23	chr10:43851200-43852000	Flanking Active TSS	A549	lung
24	chr10:43851200-43852000	Enhancers	HSMM	muscle
25	chr10:43851200-43852200	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr10:43851200-43852400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr10:43851200-43852400	Enhancers	Stomach Mucosa	stomach
28	chr10:43851400-43852000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr10:43851400-43857200	Weak transcription	Brain Substantia Nigra	brain
30	chr10:43851600-43852000	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr10:43851600-43852000	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr10:43851600-43852000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr10:43851600-43852000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr10:43851600-43852000	Enhancers	Pancreas	Pancrea
35	chr10:43851600-43852200	Enhancers	Fetal Intestine Large	intestine
36	chr10:43851800-43852000	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr10:43851800-43852200	Enhancers	Fetal Intestine Small	intestine
38	chr10:43851800-43852200	Flanking Active TSS	Hela-S3	cervix
39	chr10:43851800-43853000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr10:43851800-43856400	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr10:43851800-43856600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr10:43851800-43857000	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr10:43851800-43857000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr10:43851800-43857000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr10:43851800-43857000	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr10:43851800-43857200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr10:43851800-43857200	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr10:43851800-43857200	Weak transcription	HSMMtube	muscle

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