Variant report

Variant	rs12194095
Chromosome Location	chr6:26364520-26364521
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	RFX5	chr6:26364506-26366305	K562	blood:	n/a	chr6:26365394-26365403 chr6:26365363-26365372 chr6:26365370-26365378 chr6:26365360-26365375
2	MXI1	chr6:26364117-26367241	SK-N-SH	brain:	n/a	chr6:26365782-26365791
3	RFX5	chr6:26362983-26367827	IMR90	lung:	n/a	chr6:26365394-26365403 chr6:26365363-26365372 chr6:26365370-26365378 chr6:26365360-26365375
4	MAX	chr6:26364089-26364576	K562	blood:	n/a	n/a
5	RFX5	chr6:26364327-26366044	H1-hESC	embryonic stem cell:	n/a	chr6:26365394-26365403 chr6:26365363-26365372 chr6:26365370-26365378 chr6:26365360-26365375
6	WRNIP1	chr6:26364413-26364715	GM12878	blood:	n/a	n/a
7	MAX	chr6:26364387-26364741	NB4	blood:	n/a	n/a
8	RFX5	chr6:26362934-26367943	SK-N-SH	brain:	n/a	chr6:26365394-26365403 chr6:26365363-26365372 chr6:26365370-26365378 chr6:26365360-26365375
9	RFX5	chr6:26364309-26366049	Hela-S3	cervix:	n/a	chr6:26365394-26365403 chr6:26365363-26365372 chr6:26365370-26365378 chr6:26365360-26365375
10	RUNX3	chr6:26364458-26364900	GM12878	blood:	n/a	n/a
11	MYC	chr6:26364359-26364809	NB4	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:26361226..26362867-chr6:26363183..26365320,2	MCF-7	breast:
2	chr6:26363140..26366680-chr6:26382117..26385194,3	MCF-7	breast:
3	chr6:26360935..26366570-chr6:26520779..26523276,5	K562	blood:
4	chr6:26196455..26200961-chr6:26360873..26365378,4	K562	blood:
5	chr6:26341478..26343917-chr6:26362438..26365038,2	K562	blood:

Variant related genes	Relation type
BTN3A2	TF binding region
ENSG00000124508	Chromatin interaction
ENSG00000228223	Chromatin interaction
ENSG00000196866	Chromatin interaction
ENSG00000197409	Chromatin interaction
ENSG00000197846	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10456328	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10456330	0.85[CEU][hapmap]
rs12189841	0.81[CEU][hapmap]
rs12195971	0.81[CEU][hapmap]
rs12199239	0.81[CEU][hapmap]
rs12200782	0.81[CEU][hapmap]
rs12201802	0.81[CEU][hapmap]
rs12202419	0.81[CEU][hapmap]
rs12205731	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12207181	0.81[CEU][hapmap]
rs12208390	0.81[CEU][hapmap]
rs12211201	0.81[CEU][hapmap]
rs12213722	0.81[CEU][hapmap]
rs12216155	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3757145	0.81[CEU][hapmap]
rs3757149	0.81[CEU][hapmap]
rs3927423	0.81[CEU][hapmap]
rs72836448	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72836460	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72836467	0.89[ASN][1000 genomes]
rs72836480	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72840194	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72841519	0.95[ASN][1000 genomes]
rs7750384	0.95[ASN][1000 genomes]
rs9461246	0.81[CEU][hapmap]
rs9461249	1.00[CEU][hapmap]
rs9467741	1.00[CEU][hapmap]

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	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
4	nsv482729	chr6:26291011-26470898	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv482836	chr6:26352883-26520964	Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26356200-26365400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:26359000-26364600	Enhancers	Fetal Thymus	thymus
3	chr6:26363000-26364600	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr6:26363400-26365400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:26364000-26364800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr6:26364200-26364600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:26364200-26364600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr6:26364200-26364600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:26364200-26364600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr6:26364200-26364600	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr6:26364200-26364600	Enhancers	Primary B cells from cord blood	blood
12	chr6:26364200-26364600	Enhancers	Primary B cells from peripheral blood	blood
13	chr6:26364200-26364600	Enhancers	Muscle Satellite Cultured Cells	--
14	chr6:26364200-26364600	Enhancers	Fetal Intestine Small	intestine
15	chr6:26364200-26364600	Enhancers	Fetal Lung	lung
16	chr6:26364200-26364600	Enhancers	Fetal Muscle Leg	muscle
17	chr6:26364200-26364600	Flanking Active TSS	Right Atrium	heart
18	chr6:26364200-26364600	Enhancers	Stomach Mucosa	stomach
19	chr6:26364200-26364600	Flanking Active TSS	HepG2	liver
20	chr6:26364200-26364600	Enhancers	HMEC	breast
21	chr6:26364200-26364600	Enhancers	NHDF-Ad	bronchial
22	chr6:26364200-26364600	Enhancers	NHLF	lung
23	chr6:26364200-26364800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr6:26364200-26364800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr6:26364200-26364800	Enhancers	Esophagus	oesophagus
26	chr6:26364200-26364800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr6:26364200-26364800	Enhancers	Fetal Intestine Large	intestine
28	chr6:26364200-26364800	Enhancers	Fetal Muscle Trunk	muscle
29	chr6:26364200-26364800	Enhancers	Placenta	Placenta
30	chr6:26364200-26364800	Enhancers	Fetal Stomach	stomach
31	chr6:26364200-26364800	Enhancers	Gastric	stomach
32	chr6:26364200-26364800	Enhancers	Pancreas	Pancrea
33	chr6:26364200-26364800	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr6:26364200-26364800	Enhancers	Small Intestine	intestine
35	chr6:26364200-26364800	Enhancers	Spleen	Spleen
36	chr6:26364200-26364800	Flanking Active TSS	K562	blood
37	chr6:26364200-26365000	Flanking Active TSS	Primary T cells from cord blood	blood
38	chr6:26364200-26365000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
39	chr6:26364200-26365000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
40	chr6:26364200-26365000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
41	chr6:26364200-26365000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
42	chr6:26364200-26365000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr6:26364200-26365000	Enhancers	Left Ventricle	heart
44	chr6:26364200-26365000	Flanking Active TSS	Rectal Smooth Muscle	rectum
45	chr6:26364200-26365200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
46	chr6:26364200-26365200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
47	chr6:26364200-26365200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr6:26364200-26365200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr6:26364200-26365200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr6:26364200-26365200	Flanking Active TSS	Dnd41	blood

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