Variant report

Variant	rs708219
Chromosome Location	chr12:31543531-31543532
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:31542968..31546848-chr12:31547765..31551157,4	MCF-7	breast:
2	chr12:31476761..31479021-chr12:31542018..31543879,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139146	Chromatin interaction
ENSG00000200388	Chromatin interaction
ENSG00000177340	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10771827	0.85[EUR][1000 genomes]
rs10771828	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10771832	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10843942	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11051418	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11615961	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1259428	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12814351	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1469673	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2116704	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2568884	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2617190	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2682674	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2682680	0.83[AMR][1000 genomes]
rs2682697	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2682700	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2888762	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35906870	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4931488	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6416254	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6487989	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66521153	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs708200	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs708209	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs708214	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7134365	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs71440988	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7294574	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7302698	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7303447	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7303848	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7313158	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7313689	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7314417	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs793146	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs793154	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs793157	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs793180	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs793184	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7959877	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7962896	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7963161	0.80[AMR][1000 genomes]
rs7967832	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7968291	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7975761	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7976644	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs809407	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041877	chr12:31009451-31809254	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv541440	chr12:31009451-31809254	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	esv2751046	chr12:31174233-31684733	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv832364	chr12:31467990-31648144	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
5	esv1836923	chr12:31539122-31761172	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31535600-31560600	Weak transcription	Osteobl	bone
2	chr12:31535800-31544000	Weak transcription	Fetal Lung	lung
3	chr12:31536000-31550600	Weak transcription	Right Ventricle	heart
4	chr12:31536400-31624600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr12:31536600-31547000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr12:31536600-31577400	Weak transcription	Small Intestine	intestine
7	chr12:31537200-31546400	Strong transcription	Fetal Intestine Large	intestine
8	chr12:31537200-31555600	Strong transcription	Primary B cells from peripheral blood	blood
9	chr12:31537400-31545800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr12:31537400-31604800	Weak transcription	Spleen	Spleen
11	chr12:31537600-31544800	Strong transcription	Fetal Brain Female	brain
12	chr12:31537600-31580800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr12:31537800-31572400	Weak transcription	Stomach Mucosa	stomach
14	chr12:31538000-31544400	Strong transcription	Duodenum Mucosa	Duodenum
15	chr12:31538000-31549800	Strong transcription	A549	lung
16	chr12:31538000-31555600	Strong transcription	Liver	Liver
17	chr12:31538200-31544600	Strong transcription	Adipose Nuclei	Adipose
18	chr12:31538200-31545400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr12:31538200-31548600	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr12:31538400-31544800	Strong transcription	Brain Germinal Matrix	brain
21	chr12:31538400-31555000	Weak transcription	Brain Substantia Nigra	brain
22	chr12:31538600-31551600	Strong transcription	Fetal Intestine Small	intestine
23	chr12:31538600-31563400	Weak transcription	Colonic Mucosa	Colon
24	chr12:31538800-31544800	Strong transcription	Skeletal Muscle Female	skeletal muscle
25	chr12:31539000-31552600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr12:31539200-31543600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr12:31539400-31544600	Strong transcription	Skeletal Muscle Male	skeletal muscle
28	chr12:31539400-31545800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr12:31539400-31546400	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr12:31539600-31544200	Strong transcription	HSMM	muscle
31	chr12:31539600-31555800	Weak transcription	NH-A	brain
32	chr12:31539800-31545600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr12:31539800-31584800	Weak transcription	Fetal Heart	heart
34	chr12:31540000-31549400	Weak transcription	Brain Angular Gyrus	brain
35	chr12:31540200-31544400	Strong transcription	Brain Hippocampus Middle	brain
36	chr12:31540400-31544400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr12:31540400-31544800	Strong transcription	Brain Inferior Temporal Lobe	brain
38	chr12:31540400-31565200	Weak transcription	HUVEC	blood vessel
39	chr12:31540600-31549400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr12:31540800-31543800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr12:31540800-31544000	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr12:31540800-31544000	Weak transcription	Esophagus	oesophagus
43	chr12:31540800-31544000	Weak transcription	Hela-S3	cervix
44	chr12:31540800-31544600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr12:31540800-31545600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr12:31540800-31545800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:31540800-31545800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr12:31540800-31548600	Weak transcription	Gastric	stomach
49	chr12:31540800-31555800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr12:31540800-31563400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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