Variant report

Variant	rs12190575
Chromosome Location	chr6:56920804-56920805
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:56918758..56920870-chr6:56963743..56966191,2	K562	blood:

Extended variants
information (count: 59 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1020550	0.90[ASN][1000 genomes]
rs1044670	0.88[CEU][hapmap]
rs10456192	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10484410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11398	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs12192222	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12194288	0.90[ASN][1000 genomes]
rs12194407	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12198801	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12201039	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12211901	0.90[ASN][1000 genomes]
rs12214119	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12214882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1411578	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs1547226	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16888392	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.86[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs17619360	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800018	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.90[ASN][1000 genomes]
rs3800023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800025	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3957366	0.88[CEU][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs3996934	0.90[ASN][1000 genomes]
rs3996935	0.90[ASN][1000 genomes]
rs3996936	0.90[ASN][1000 genomes]
rs4523090	0.90[ASN][1000 genomes]
rs4631287	0.90[ASN][1000 genomes]
rs6459178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6902125	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6918222	0.86[EUR][1000 genomes]
rs6936506	0.81[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6936560	0.81[EUR][1000 genomes]
rs72868608	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73463742	0.80[ASN][1000 genomes]
rs7744148	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7748120	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7748453	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7753547	0.90[ASN][1000 genomes]
rs7756421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7764446	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7771115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9349841	0.85[ASN][1000 genomes]
rs9396247	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9396256	0.90[ASN][1000 genomes]
rs986245	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1021651	chr6:56569444-56966319	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv538228	chr6:56569444-56966319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	esv3430228	chr6:56830972-57079281	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv1026524	chr6:56902544-56951703	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS 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 miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv970717	chr6:56903957-56955783	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	nsv885913	chr6:56910884-56954439	Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
10	nsv970684	chr6:56912349-56953340	Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
11	esv3374787	chr6:56912959-56955113	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
12	esv2763988	chr6:56913072-56952630	Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
13	nsv603189	chr6:56913453-56950609	Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
14	nsv538230	chr6:56913943-56951703	Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
15	nsv526143	chr6:56917538-56954439	Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12190575	BEND6	cis	parietal	SCAN
rs12190575	RAB23	Cis_1M	lymphoblastoid	RTeQTL
rs12190575	RAB23	cis	lymphoblastoid	seeQTL
rs12190575	KIAA1586	Cis_1M	lymphoblastoid	RTeQTL
rs12190575	BEND6	cis	cerebellum	SCAN
rs12190575	BEND6	cis	Muscle Skeletal	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56911600-56925000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:56911600-56935200	Weak transcription	Gastric	stomach
3	chr6:56911600-56939800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:56911800-56922200	Weak transcription	Right Ventricle	heart
5	chr6:56911800-56924200	Weak transcription	Colonic Mucosa	Colon
6	chr6:56911800-56930800	Weak transcription	Psoas Muscle	Psoas
7	chr6:56911800-56934200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr6:56911800-56936200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:56911800-56943000	Weak transcription	Esophagus	oesophagus
10	chr6:56913400-56921400	Strong transcription	HSMM	muscle
11	chr6:56913400-56924400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr6:56913400-56940600	Weak transcription	Brain Substantia Nigra	brain
13	chr6:56913600-56921600	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr6:56913600-56921800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr6:56913600-56924600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr6:56913600-56925600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr6:56913600-56926600	Weak transcription	Small Intestine	intestine
18	chr6:56913600-56931600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:56913600-56934000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr6:56913600-56941600	Weak transcription	Brain Anterior Caudate	brain
21	chr6:56913800-56928000	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr6:56913800-56930600	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr6:56914000-56934600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr6:56914200-56927000	Strong transcription	Osteobl	bone
25	chr6:56914200-56927400	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr6:56914200-56929600	Weak transcription	Fetal Brain Male	brain
27	chr6:56914200-56931000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr6:56914200-56934200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:56914400-56921400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr6:56914400-56922200	Strong transcription	Liver	Liver
31	chr6:56914400-56923200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr6:56914400-56928600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr6:56914400-56929000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr6:56914400-56931800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr6:56914400-56935000	Weak transcription	Fetal Kidney	kidney
36	chr6:56914600-56927600	Strong transcription	Dnd41	blood
37	chr6:56914600-56954200	Weak transcription	Rectal Smooth Muscle	rectum
38	chr6:56914800-56924600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr6:56915000-56930200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr6:56915000-56932000	Strong transcription	Placenta	Placenta
41	chr6:56915000-56940200	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr6:56915200-56921000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr6:56915200-56921800	Strong transcription	K562	blood
44	chr6:56915200-56922000	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr6:56915200-56922800	Strong transcription	Fetal Muscle Trunk	muscle
46	chr6:56915200-56923000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr6:56915400-56921000	Strong transcription	Primary hematopoietic stem cells	blood
48	chr6:56915400-56922000	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr6:56915400-56923200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr6:56915400-56929400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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