Variant report

Variant	rs2700505
Chromosome Location	chr12:104349688-104349689
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104348297..104351124-chr12:104530392..104533056,3	MCF-7	breast:
2	chr12:104233713..104237034-chr12:104348727..104352026,4	MCF-7	breast:
3	chr12:104234122..104238773-chr12:104347839..104352988,5	MCF-7	breast:
4	chr12:104348328..104351209-chr12:104680724..104683661,2	K562	blood:
5	chr12:104320418..104331406-chr12:104346801..104355501,25	MCF-7	breast:

Variant related genes	Relation type
ENSG00000265072	Chromatin interaction
ENSG00000120837	Chromatin interaction
ENSG00000257327	Chromatin interaction
ENSG00000166598	Chromatin interaction
ENSG00000111696	Chromatin interaction
ENSG00000198431	Chromatin interaction
ENSG00000214198	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10861149	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11111852	0.94[ASN][1000 genomes]
rs11111854	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs1165692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1165693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs1165694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1165695	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1165696	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1177457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1179177	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12227567	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs15805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293617	0.96[ASN][1000 genomes]
rs2293618	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2576975	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2583254	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2583262	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2583264	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2700508	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2700509	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2722190	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2722191	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2722192	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964375	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs703657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv427922	chr12:104325583-104523096	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2700505	KRTHB5	Cis_1M	lymphoblastoid	RTeQTL
rs2700505	C12orf73	cis	Artery Aorta	GTEx
rs2700505	C12orf73	cis	Artery Tibial	GTEx
rs2700505	C12orf73	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104325600-104349800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:104337000-104350000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:104346200-104349800	Weak transcription	Right Atrium	heart
4	chr12:104347400-104349800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:104347600-104349800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:104347600-104349800	Weak transcription	Esophagus	oesophagus
7	chr12:104347600-104350000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:104347800-104349800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr12:104348000-104349800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr12:104348200-104349800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr12:104348400-104349800	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr12:104348400-104349800	Weak transcription	Lung	lung
13	chr12:104348400-104349800	Weak transcription	Pancreas	Pancrea
14	chr12:104348400-104349800	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr12:104348400-104350000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr12:104348400-104350000	Weak transcription	Aorta	Aorta
17	chr12:104348400-104350200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr12:104348600-104349800	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr12:104348600-104349800	Weak transcription	Placenta	Placenta
20	chr12:104348600-104349800	Weak transcription	Ovary	ovary
21	chr12:104348600-104349800	Weak transcription	Spleen	Spleen
22	chr12:104348800-104349800	Enhancers	Primary T cells fromperipheralblood	blood
23	chr12:104348800-104349800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr12:104349000-104349800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr12:104349000-104349800	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr12:104349000-104349800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr12:104349000-104349800	Enhancers	Liver	Liver
28	chr12:104349000-104349800	Enhancers	Fetal Muscle Trunk	muscle
29	chr12:104349000-104350000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr12:104349000-104350000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr12:104349000-104350000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr12:104349000-104350000	Enhancers	Small Intestine	intestine
33	chr12:104349200-104349800	Enhancers	Colon Smooth Muscle	Colon
34	chr12:104349200-104349800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr12:104349200-104349800	Enhancers	Right Ventricle	heart
36	chr12:104349200-104350000	Enhancers	Gastric	stomach
37	chr12:104349200-104350400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr12:104349200-104350400	Flanking Active TSS	Dnd41	blood
39	chr12:104349200-104351200	Active TSS	NHLF	lung
40	chr12:104349200-104351600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr12:104349200-104351600	Active TSS	iPS-20b Cell Line	embryonic stem cell
42	chr12:104349200-104351600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr12:104349200-104351800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr12:104349400-104349800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr12:104349400-104349800	Enhancers	Primary hematopoietic stem cells	blood
46	chr12:104349400-104349800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr12:104349400-104349800	Active TSS	Brain Germinal Matrix	brain
48	chr12:104349400-104349800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr12:104349400-104349800	Enhancers	Fetal Intestine Small	intestine
50	chr12:104349400-104349800	Enhancers	Fetal Muscle Leg	muscle

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