Variant report

Variant	rs12217904
Chromosome Location	chr10:43873063-43873064
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:43572567..43574576-chr10:43871912..43874300,2	MCF-7	breast:
2	chr10:43872575..43876095-chr10:43882284..43884232,3	MCF-7	breast:
3	chr10:43872190..43874613-chr10:43876662..43879551,2	MCF-7	breast:
4	chr10:43871156..43873065-chr10:43900676..43903339,2	MCF-7	breast:
5	chr10:43871402..43874267-chr10:43884801..43886478,2	MCF-7	breast:
6	chr10:43871509..43873780-chr10:43874816..43877105,2	K562	blood:
7	chr10:43867647..43875264-chr10:43900659..43906151,11	MCF-7	breast:
8	chr10:43787068..43788733-chr10:43871356..43873584,2	MCF-7	breast:
9	chr10:43868700..43874062-chr10:43890607..43893448,6	MCF-7	breast:
10	chr10:43868968..43875759-chr10:43890269..43893335,11	MCF-7	breast:
11	chr10:43632845..43635197-chr10:43871266..43873181,2	MCF-7	breast:
12	chr10:43853521..43859723-chr10:43870896..43875408,11	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000169813	Chromatin interaction
ENSG00000169826	Chromatin interaction
ENSG00000273008	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10409	0.82[YRI][hapmap]
rs10899796	0.82[ASN][1000 genomes]
rs10899803	0.82[YRI][hapmap]
rs10899807	0.82[YRI][hapmap]
rs11238515	0.85[ASN][1000 genomes]
rs11238530	0.81[ASN][1000 genomes]
rs11238553	0.82[YRI][hapmap]
rs11814409	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1879312	0.92[ASN][1000 genomes]
rs57059251	0.82[EUR][1000 genomes]
rs59806733	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
3	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
4	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
5	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
6	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
7	nsv895088	chr10:43871999-44003101	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43858600-43891000	Weak transcription	Right Atrium	heart
2	chr10:43867200-43876200	Weak transcription	Hela-S3	cervix
3	chr10:43868200-43873400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr10:43869000-43880400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr10:43869200-43882000	Weak transcription	Left Ventricle	heart
6	chr10:43869400-43880200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr10:43869600-43873800	Enhancers	Placenta	Placenta
8	chr10:43869800-43878600	Weak transcription	A549	lung
9	chr10:43870000-43881200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr10:43870000-43882000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr10:43870200-43881000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr10:43870200-43882000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr10:43870200-43882000	Weak transcription	Brain Substantia Nigra	brain
14	chr10:43870400-43880000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr10:43870400-43881000	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr10:43870400-43881600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr10:43870400-43882000	Weak transcription	Brain Angular Gyrus	brain
18	chr10:43870800-43873800	Enhancers	Placenta Amnion	Placenta Amnion
19	chr10:43871000-43880400	Weak transcription	Brain Anterior Caudate	brain
20	chr10:43871200-43873400	Enhancers	H1 Cell Line	embryonic stem cell
21	chr10:43871200-43873800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr10:43871200-43881600	Weak transcription	Brain Hippocampus Middle	brain
23	chr10:43871400-43880800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr10:43871600-43880000	Weak transcription	Fetal Muscle Leg	muscle
25	chr10:43871800-43879600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr10:43872000-43873400	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr10:43872200-43873400	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr10:43872200-43873400	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr10:43872200-43880200	Weak transcription	Lung	lung
30	chr10:43872400-43873400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr10:43872400-43873400	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr10:43872400-43873400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr10:43872400-43873600	Enhancers	Fetal Intestine Large	intestine
34	chr10:43872400-43873600	Enhancers	Fetal Intestine Small	intestine
35	chr10:43872400-43874000	Flanking Active TSS	HepG2	liver
36	chr10:43872600-43873200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr10:43872600-43873200	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr10:43872600-43873200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr10:43872600-43873200	Enhancers	Stomach Mucosa	stomach
40	chr10:43872600-43873400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
41	chr10:43872600-43874000	Enhancers	K562	blood
42	chr10:43872600-43881000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr10:43872800-43873200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr10:43872800-43873200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr10:43872800-43873200	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr10:43872800-43873200	Enhancers	Gastric	stomach
47	chr10:43873000-43873800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links