Variant report

Variant	rs11830643
Chromosome Location	chr12:39748847-39748848
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:39747712..39750921-chr12:39754829..39757616,3	K562	blood:
2	chr12:39742374..39745219-chr12:39747056..39748871,3	K562	blood:
3	chr12:39746862..39749786-chr12:39834162..39836937,2	K562	blood:
4	chr12:39747731..39750258-chr12:39836308..39838380,2	K562	blood:
5	chr12:39748533..39750921-chr12:39755964..39757616,2	K562	blood:
6	chr12:39746719..39749261-chr12:39836622..39838192,2	MCF-7	breast:
7	chr12:39734809..39736531-chr12:39748406..39750857,2	K562	blood:

Variant related genes	Relation type
ENSG00000139116	Chromatin interaction
ENSG00000252974	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10876868	0.83[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10876876	0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10876886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10876972	0.94[ASW][hapmap];0.96[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap]
rs11171674	0.83[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11171675	0.87[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11171676	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11171720	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]
rs11171730	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11171789	0.87[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11171891	0.87[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11171901	0.81[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11171923	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11171938	0.83[CEU][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11172108	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[ASN][1000 genomes]
rs11172120	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.81[ASN][1000 genomes]
rs11172183	0.81[CEU][hapmap];0.94[JPT][hapmap]
rs11172282	0.83[CEU][hapmap];0.95[JPT][hapmap]
rs11172492	0.96[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs11836755	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12228767	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12230604	0.83[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12424345	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1512936	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1512942	0.86[ASN][1000 genomes]
rs1567739	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17127019	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1828653	0.83[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1955314	0.81[ASN][1000 genomes]
rs2388320	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3736466	0.87[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4320988	0.96[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs4492858	0.94[ASW][hapmap];0.96[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap]
rs4500523	0.91[CEU][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap]
rs57756176	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57833783	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58240943	0.83[ASN][1000 genomes]
rs58613501	0.81[ASN][1000 genomes]
rs60792848	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7137143	0.87[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73094410	0.81[ASN][1000 genomes]
rs7953548	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7962283	0.95[CEU][hapmap];0.92[YRI][hapmap];0.81[ASN][1000 genomes]
rs7964447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7965222	0.81[ASN][1000 genomes]
rs7968837	0.88[ASW][hapmap];0.96[CEU][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.93[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap]
rs7971515	0.88[ASN][1000 genomes]
rs7979329	0.88[ASN][1000 genomes]
rs7979444	0.83[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs958914	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][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	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
2	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
3	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
4	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
5	nsv558590	chr12:39724344-39751273	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11830643	KIF21A	cis	cerebellum	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39696600-39762200	Weak transcription	Fetal Brain Male	brain
2	chr12:39697800-39771800	Weak transcription	Fetal Kidney	kidney
3	chr12:39699600-39760600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr12:39718400-39756800	Weak transcription	HSMM	muscle
5	chr12:39721000-39770600	Weak transcription	Gastric	stomach
6	chr12:39721600-39752400	Weak transcription	Right Ventricle	heart
7	chr12:39722800-39767200	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr12:39724400-39751800	Weak transcription	Fetal Heart	heart
9	chr12:39725000-39750000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr12:39725200-39753600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr12:39725800-39749800	Weak transcription	K562	blood
12	chr12:39726000-39753800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr12:39726400-39749800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr12:39726400-39766600	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr12:39726600-39766600	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr12:39726600-39766600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr12:39726600-39766800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr12:39726800-39749800	Weak transcription	Brain Hippocampus Middle	brain
19	chr12:39726800-39762200	Weak transcription	Placenta	Placenta
20	chr12:39726800-39766600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr12:39727000-39749000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr12:39727000-39749400	Weak transcription	Adipose Nuclei	Adipose
23	chr12:39727000-39749800	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr12:39727000-39750000	Weak transcription	Brain Anterior Caudate	brain
25	chr12:39727000-39750000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr12:39727000-39751000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr12:39727000-39751800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:39727000-39753800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr12:39727000-39755400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr12:39727000-39755600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr12:39727000-39758000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr12:39727000-39758000	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr12:39727000-39758200	Weak transcription	Fetal Intestine Large	intestine
34	chr12:39727000-39760600	Weak transcription	Brain Angular Gyrus	brain
35	chr12:39727000-39761400	Weak transcription	Fetal Intestine Small	intestine
36	chr12:39727000-39762400	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr12:39727000-39767000	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr12:39727000-39779200	Weak transcription	Aorta	Aorta
39	chr12:39727200-39749800	Weak transcription	Duodenum Mucosa	Duodenum
40	chr12:39728800-39750200	Weak transcription	Hela-S3	cervix
41	chr12:39733000-39750000	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr12:39733600-39749200	Weak transcription	Fetal Brain Female	brain
43	chr12:39734600-39749000	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr12:39735200-39761400	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr12:39735600-39749000	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr12:39735600-39750400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr12:39735600-39755800	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr12:39735600-39766600	Weak transcription	HMEC	breast
49	chr12:39735600-39766600	Weak transcription	NHEK	skin
50	chr12:39736200-39749000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links