Variant report

Variant	rs12191672
Chromosome Location	chr6:36929007-36929008
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr6:36926981-36929129	K562	blood:	n/a	chr6:36928483-36928495 chr6:36928485-36928493 chr6:36928484-36928494 chr6:36928484-36928494

No.	Distal block	Cell Line	Cell type
1	chr6:36927877..36929590-chr6:36935143..36936751,2	MCF-7	breast:
2	chr6:36920733..36923639-chr6:36925448..36929945,7	K562	blood:
3	chr6:36928773..36930576-chr6:36930676..36932270,2	MCF-7	breast:
4	chr6:36926514..36929766-chr6:36952495..36955671,4	MCF-7	breast:
5	chr6:36562786..36564332-chr6:36928250..36929910,2	K562	blood:
6	chr6:36921774..36924130-chr6:36928401..36929929,2	MCF-7	breast:
7	chr6:36928588..36930558-chr6:36986253..36988587,2	K562	blood:
8	chr6:36926516..36929397-chr6:36985217..36986948,2	K562	blood:
9	chr6:36852067..36855564-chr6:36924677..36929209,4	K562	blood:

Variant related genes	Relation type
PI16	TF binding region
ENSG00000164530	Chromatin interaction
ENSG00000137409	Chromatin interaction
ENSG00000198663	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1023037	0.89[ASN][1000 genomes]
rs12199301	1.00[JPT][hapmap]
rs17624546	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17624895	0.81[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs2177845	0.89[ASN][1000 genomes]
rs2293388	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs2293389	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs3778022	1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.80[EUR][1000 genomes]
rs3778024	0.82[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3778026	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3798477	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs3798478	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4585544	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6901560	0.81[GIH][hapmap];0.83[MEX][hapmap]
rs726819	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs734905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs753634	0.81[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs753635	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7755143	0.93[GIH][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9357232	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9380628	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	nsv1030015	chr6:36818510-37104446	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv916833	chr6:36826524-37029833	Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv885815	chr6:36915906-36979583	Active TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12191672	PI16	cis	cerebellum	SCAN
rs12191672	PI16	cis	parietal	SCAN
rs12191672	LPAR6	trans	lymphoblastoid	seeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36917600-36931200	Weak transcription	Brain Hippocampus Middle	brain
2	chr6:36921800-36931200	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr6:36922000-36931000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr6:36922200-36929200	Weak transcription	Spleen	Spleen
5	chr6:36923400-36930600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr6:36923400-36930600	Weak transcription	GM12878-XiMat	blood
7	chr6:36923400-36931000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr6:36923400-36931000	Weak transcription	Brain Substantia Nigra	brain
9	chr6:36924400-36929200	Weak transcription	Right Atrium	heart
10	chr6:36924600-36930000	Weak transcription	Primary B cells from cord blood	blood
11	chr6:36924800-36930600	Weak transcription	Primary T cells from cord blood	blood
12	chr6:36927000-36929400	Enhancers	K562	blood
13	chr6:36927000-36931600	Weak transcription	Lung	lung
14	chr6:36927200-36929200	Weak transcription	Gastric	stomach
15	chr6:36927200-36930400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr6:36927200-36930400	Enhancers	Fetal Thymus	thymus
17	chr6:36927200-36931000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr6:36927200-36931600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:36927200-36933400	Enhancers	Stomach Mucosa	stomach
20	chr6:36927400-36929200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr6:36927400-36929400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr6:36927400-36931000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr6:36927600-36929200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr6:36927800-36929200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr6:36927800-36929200	Enhancers	NH-A	brain
26	chr6:36927800-36929200	Enhancers	NHEK	skin
27	chr6:36927800-36929400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr6:36927800-36929400	Enhancers	Duodenum Mucosa	Duodenum
29	chr6:36927800-36929800	Enhancers	Fetal Heart	heart
30	chr6:36927800-36933200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr6:36928000-36929400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr6:36928000-36929600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr6:36928000-36931200	Weak transcription	Stomach Smooth Muscle	stomach
34	chr6:36928000-36933600	Enhancers	Primary T cells fromperipheralblood	blood
35	chr6:36928200-36929400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr6:36928200-36929600	Enhancers	Placenta Amnion	Placenta Amnion
37	chr6:36928200-36935200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr6:36928400-36929200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr6:36928400-36929200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr6:36928400-36929400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr6:36928400-36929400	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr6:36928400-36929400	Enhancers	Placenta	Placenta
43	chr6:36928400-36929400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
44	chr6:36928400-36929400	Bivalent Enhancer	HepG2	liver
45	chr6:36928400-36929600	Enhancers	Thymus	Thymus
46	chr6:36928400-36929800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr6:36928600-36929200	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr6:36928600-36929200	Enhancers	Fetal Intestine Small	intestine
49	chr6:36928600-36929200	Enhancers	HMEC	breast
50	chr6:36928600-36929400	Enhancers	Left Ventricle	heart

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