Variant report

Variant	rs10861369
Chromosome Location	chr12:105670337-105670338
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:105666902..105668565-chr12:105668821..105670480,2	MCF-7	breast:
2	chr12:105669318..105671725-chr12:105671991..105674954,2	K562	blood:
3	chr12:105628689..105630272-chr12:105669030..105671584,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235162	Chromatin interaction
ENSG00000136044	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10778376	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10778380	0.96[ASN][1000 genomes]
rs10861365	0.90[ASN][1000 genomes]
rs10861366	0.92[ASN][1000 genomes]
rs10861368	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112418	0.80[ASN][1000 genomes]
rs11112435	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11112439	0.98[ASN][1000 genomes]
rs11112441	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12228302	0.91[ASN][1000 genomes]
rs12306463	0.99[ASN][1000 genomes]
rs12315510	0.96[ASN][1000 genomes]
rs12321534	0.87[CEU][hapmap]
rs12322134	0.84[CHB][hapmap];0.80[ASN][1000 genomes]
rs3794232	0.84[CHB][hapmap];0.80[ASN][1000 genomes]
rs56043130	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6539199	0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7134323	0.96[ASN][1000 genomes]
rs7138073	0.99[ASN][1000 genomes]
rs73181847	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7488014	1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs7955095	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7966106	0.84[CHB][hapmap];0.80[ASN][1000 genomes]
rs7972263	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975125	0.81[ASN][1000 genomes]
rs7975197	0.99[ASN][1000 genomes]
rs7978034	0.82[CEU][hapmap]
rs9634185	0.83[CHB][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899499	chr12:105616297-105722529	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1044450	chr12:105668451-105682822	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv510589	chr12:105670071-105743755	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10861369	TCP11L2	cis	parietal	SCAN
rs10861369	ARL1	cis	cerebellum	SCAN
rs10861369	KIAA1033	cis	cerebellum	SCAN
rs10861369	KIAA1033	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105659600-105672200	Weak transcription	Aorta	Aorta
2	chr12:105664600-105672200	Weak transcription	HSMM	muscle
3	chr12:105665000-105674200	Weak transcription	Osteobl	bone
4	chr12:105665600-105674800	Weak transcription	NHDF-Ad	bronchial
5	chr12:105668200-105671800	Weak transcription	Fetal Intestine Small	intestine
6	chr12:105668200-105674800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr12:105668600-105673400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:105669800-105670400	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr12:105669800-105670600	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr12:105669800-105670600	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr12:105670000-105670400	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr12:105670000-105670400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:105670000-105670400	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr12:105670000-105670400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr12:105670000-105670400	Enhancers	NHEK	skin
16	chr12:105670000-105670800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr12:105670200-105670600	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr12:105670200-105670600	Enhancers	Psoas Muscle	Psoas
19	chr12:105670200-105670600	Enhancers	HMEC	breast
20	chr12:105670200-105670800	Enhancers	Skeletal Muscle Female	skeletal muscle

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