Variant report

Variant	rs11171720
Chromosome Location	chr12:39710473-39710474
allele	C/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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:39701435..39705436-chr12:39706649..39711644,6	MCF-7	breast:
2	chr12:39708828..39711217-chr12:39835849..39838225,2	K562	blood:
3	chr12:39701621..39703209-chr12:39709361..39712125,2	K562	blood:
4	chr12:39709526..39712296-chr12:39716470..39718844,2	MCF-7	breast:
5	chr12:39708256..39710912-chr12:39833762..39835679,2	MCF-7	breast:
6	chr12:39701709..39705031-chr12:39707216..39710861,3	K562	blood:
7	chr12:39708405..39711742-chr12:39713944..39715751,3	K562	blood:
8	chr12:39705679..39708570-chr12:39709976..39712207,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000252974	Chromatin interaction
ENSG00000139116	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10876868	0.94[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10876876	0.94[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10876886	0.87[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10876972	0.84[CEU][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs11171674	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11171675	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11171676	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11171730	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11171789	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11171891	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11171901	0.94[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11171923	0.84[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11171938	0.95[CEU][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11172108	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs11172120	0.84[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap]
rs11172183	0.95[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs11172282	0.95[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs11830643	0.87[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11836755	0.90[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12228767	0.87[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12230604	0.94[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12424345	0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1512936	0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1512942	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1567739	0.84[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17127019	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1828653	0.95[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1955314	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2388320	0.84[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3736466	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4320988	0.84[CEU][hapmap];0.95[JPT][hapmap]
rs4492858	0.84[CEU][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs4500523	0.86[GIH][hapmap];0.95[JPT][hapmap]
rs57756176	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57833783	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59695906	0.81[AMR][1000 genomes]
rs60792848	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7137143	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7953548	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7962283	0.83[CEU][hapmap]
rs7964447	0.87[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7971515	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7974928	0.91[CEU][hapmap];0.86[CHB][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs7979329	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7979444	0.88[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.81[ASN][1000 genomes]
rs958914	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899013	chr12:39567945-39732430	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv832375	chr12:39599362-39784722	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv832376	chr12:39633080-39808277	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv470286	chr12:39651893-39729700	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv558589	chr12:39667861-39768356	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv531527	chr12:39680812-40182822	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11171720	KIF21A	cis	multi-tissue	Pritchard
rs11171720	KIF21A	cis	cerebellum	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39685200-39714400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr12:39686600-39722400	Weak transcription	GM12878-XiMat	blood
3	chr12:39686600-39725400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr12:39686800-39729800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr12:39686800-39738800	Weak transcription	Pancreas	Pancrea
6	chr12:39687200-39726400	Weak transcription	Fetal Intestine Small	intestine
7	chr12:39687600-39723800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr12:39688400-39724600	Weak transcription	Esophagus	oesophagus
9	chr12:39688400-39726400	Weak transcription	Aorta	Aorta
10	chr12:39689000-39724000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr12:39689600-39725400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr12:39690400-39715200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:39690600-39711600	Weak transcription	Placenta	Placenta
14	chr12:39695000-39726400	Weak transcription	Fetal Intestine Large	intestine
15	chr12:39695000-39726400	Weak transcription	HepG2	liver
16	chr12:39695600-39724000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr12:39695600-39742000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr12:39696600-39762200	Weak transcription	Fetal Brain Male	brain
19	chr12:39696800-39712000	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr12:39697600-39711000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr12:39697800-39771800	Weak transcription	Fetal Kidney	kidney
22	chr12:39698000-39724400	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr12:39698200-39724400	Weak transcription	K562	blood
24	chr12:39698600-39724000	Weak transcription	Brain Anterior Caudate	brain
25	chr12:39698600-39724000	Weak transcription	Brain Substantia Nigra	brain
26	chr12:39698600-39725200	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr12:39698600-39725400	Weak transcription	Brain Hippocampus Middle	brain
28	chr12:39698800-39711000	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr12:39699600-39724600	Weak transcription	Brain Angular Gyrus	brain
30	chr12:39699600-39760600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr12:39700000-39721400	Weak transcription	Fetal Heart	heart
32	chr12:39700600-39723400	Weak transcription	Adipose Nuclei	Adipose
33	chr12:39700600-39724000	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr12:39700800-39724000	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr12:39701000-39711000	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr12:39701000-39726400	Weak transcription	Left Ventricle	heart
37	chr12:39701200-39716400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr12:39701400-39724000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr12:39701600-39716400	Weak transcription	Brain Germinal Matrix	brain
40	chr12:39701600-39718200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr12:39701600-39723800	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr12:39701600-39723800	Weak transcription	Brain Cingulate Gyrus	brain
43	chr12:39701600-39724000	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr12:39701600-39725000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr12:39701800-39713000	Weak transcription	Fetal Brain Female	brain
46	chr12:39701800-39724400	Weak transcription	HMEC	breast
47	chr12:39703200-39711200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr12:39704200-39746200	Weak transcription	HUVEC	blood vessel
49	chr12:39704600-39718800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr12:39704600-39723200	Weak transcription	NHEK	skin

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