Variant report

Variant	rs2307062
Chromosome Location	chr12:46756239-46756240
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:46662773..46664298-chr12:46755324..46757349,2	MCF-7	breast:
2	chr12:46663312..46666406-chr12:46754623..46758323,3	K562	blood:

Variant related genes	Relation type
ENSG00000111371	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10467215	0.82[CHB][hapmap]
rs10506267	0.83[CHB][hapmap];1.00[EUR][1000 genomes]
rs10506268	1.00[EUR][1000 genomes]
rs11183454	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11183467	0.88[CHB][hapmap];0.86[CHD][hapmap]
rs11183482	0.88[CHB][hapmap];0.86[CHD][hapmap]
rs11183500	0.82[CHB][hapmap]
rs11183510	0.82[CHB][hapmap]
rs1125908	1.00[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11830769	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11834593	0.82[ASN][1000 genomes]
rs11834905	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11837634	0.85[YRI][hapmap]
rs12299499	0.84[CHB][hapmap]
rs12317255	0.88[CHB][hapmap];0.86[CHD][hapmap]
rs12321512	0.94[CHB][hapmap]
rs12321960	0.82[CHB][hapmap]
rs13377959	0.88[CHB][hapmap];0.83[CHD][hapmap]
rs17096884	1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17096896	0.94[CHB][hapmap]
rs17096922	0.88[CHB][hapmap]
rs1948425	0.84[JPT][hapmap]
rs2125646	1.00[ASW][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2307059	0.84[JPT][hapmap]
rs2307063	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2408509	0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3742061	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3935048	0.82[CHD][hapmap]
rs56222195	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57067899	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57149475	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57271454	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57425661	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60628240	1.00[EUR][1000 genomes]
rs60977966	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61232019	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61406609	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61517444	1.00[EUR][1000 genomes]
rs73282532	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73282561	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73282591	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs74083707	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74083710	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74084031	1.00[EUR][1000 genomes]
rs7953339	0.82[CHB][hapmap]
rs7954314	0.88[CHB][hapmap];0.83[CHD][hapmap]
rs7967889	0.88[CHB][hapmap]
rs7980023	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs923788	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832398	chr12:46611692-46825530	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	esv1842882	chr12:46691487-47009428	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
3	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription 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	152 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46737600-46761200	Weak transcription	Gastric	stomach
2	chr12:46744000-46760600	Weak transcription	Spleen	Spleen
3	chr12:46746000-46756800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:46748800-46764200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:46749000-46757600	Weak transcription	Stomach Mucosa	stomach
6	chr12:46750400-46761200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr12:46751600-46756600	Weak transcription	Thymus	Thymus
8	chr12:46751600-46760600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr12:46751600-46761200	Strong transcription	Fetal Brain Female	brain
10	chr12:46751800-46757400	Strong transcription	HSMM	muscle
11	chr12:46751800-46759200	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr12:46752000-46757800	Genic enhancers	A549	lung
13	chr12:46752200-46761200	Strong transcription	Placenta	Placenta
14	chr12:46752400-46756800	Strong transcription	Adipose Nuclei	Adipose
15	chr12:46752400-46756800	Strong transcription	Osteobl	bone
16	chr12:46752400-46758600	Strong transcription	Rectal Mucosa Donor 31	rectum
17	chr12:46752400-46759000	Strong transcription	Colonic Mucosa	Colon
18	chr12:46752400-46759800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr12:46752400-46760400	Strong transcription	Brain Germinal Matrix	brain
20	chr12:46752400-46761400	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr12:46752400-46761600	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr12:46752400-46761600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr12:46752400-46761800	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr12:46752400-46764200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr12:46752600-46757000	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr12:46752600-46757400	Strong transcription	Placenta Amnion	Placenta Amnion
27	chr12:46752600-46758000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr12:46752600-46758000	Strong transcription	Brain Inferior Temporal Lobe	brain
29	chr12:46752600-46758000	Strong transcription	Stomach Smooth Muscle	stomach
30	chr12:46752600-46758800	Strong transcription	Duodenum Mucosa	Duodenum
31	chr12:46752600-46758800	Strong transcription	Fetal Intestine Large	intestine
32	chr12:46752600-46758800	Strong transcription	NH-A	brain
33	chr12:46752600-46759000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr12:46752600-46759000	Strong transcription	Fetal Lung	lung
35	chr12:46752600-46759200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr12:46752600-46759400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr12:46752600-46760600	Strong transcription	Fetal Thymus	thymus
38	chr12:46752600-46761200	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr12:46752600-46761200	Strong transcription	Fetal Muscle Leg	muscle
40	chr12:46752600-46761400	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr12:46752600-46761600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr12:46752600-46762400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr12:46752600-46763000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr12:46752600-46763600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr12:46752600-46764200	Strong transcription	Fetal Muscle Trunk	muscle
46	chr12:46752800-46757600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr12:46752800-46758000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr12:46752800-46759000	Strong transcription	HSMMtube	muscle
49	chr12:46752800-46759400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr12:46752800-46759600	Strong transcription	Sigmoid Colon	Sigmoid Colon

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