Variant report

Variant	rs12198692
Chromosome Location	chr6:15340471-15340472
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:15339598..15341681-chr6:15358454..15361224,2	K562	blood:
2	chr6:15339473..15343526-chr6:15347239..15351934,4	K562	blood:
3	chr6:15247363..15250406-chr6:15339342..15342224,4	K562	blood:
4	chr6:15337898..15340575-chr6:15344754..15346460,2	K562	blood:
5	chr6:15334385..15336303-chr6:15339502..15341562,2	K562	blood:

Variant related genes	Relation type
ENSG00000008083	Chromatin interaction
ENSG00000235488	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10949292	0.84[EUR][1000 genomes]
rs10949294	1.00[CHB][hapmap]
rs10949295	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs11753952	0.82[EUR][1000 genomes]
rs11759040	1.00[JPT][hapmap]
rs11759478	0.82[CEU][hapmap];1.00[CHB][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12192599	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12198694	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12199895	0.91[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12201889	1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12204124	1.00[JPT][hapmap]
rs12206745	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12209228	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12209748	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12210592	0.82[CEU][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12211278	1.00[CHB][hapmap]
rs12211777	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12212013	0.83[ASN][1000 genomes]
rs12214719	0.84[EUR][1000 genomes]
rs12215596	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12215740	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13192347	1.00[CHB][hapmap]
rs13194410	1.00[CHB][hapmap]
rs13205396	1.00[CHB][hapmap]
rs13205612	1.00[CHB][hapmap]
rs16876250	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16876278	1.00[CHB][hapmap]
rs17575737	0.82[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes]
rs17576233	1.00[CHB][hapmap]
rs17576436	1.00[CHB][hapmap]
rs17619730	1.00[JPT][hapmap]
rs17619838	0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17637773	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs17638192	1.00[CHB][hapmap]
rs17687211	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17713010	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs55634912	0.83[ASN][1000 genomes]
rs55980198	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6902997	0.93[AMR][1000 genomes]
rs6919296	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6935879	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6938919	0.82[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs72834590	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7765425	1.00[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027010	chr6:15201803-15425629	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv538140	chr6:15217899-15547127	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers 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	29 gene(s)	inside rSNPs	diseases
3	nsv1030558	chr6:15234675-15449137	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv538141	chr6:15234675-15509163	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv538142	chr6:15243960-15404893	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv949448	chr6:15279490-15449441	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv1025512	chr6:15291551-15452395	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv538143	chr6:15291551-15452395	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv538144	chr6:15310696-15364984	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15327800-15375800	Weak transcription	Aorta	Aorta
2	chr6:15328000-15342000	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr6:15328200-15340800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr6:15329200-15341000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr6:15329800-15343600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr6:15330800-15348800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr6:15331400-15340800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr6:15331400-15341600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr6:15331600-15345400	Weak transcription	Ovary	ovary
10	chr6:15331600-15346000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr6:15331600-15347000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:15331800-15340600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr6:15331800-15340800	Weak transcription	NHEK	skin
14	chr6:15332000-15355800	Weak transcription	Fetal Muscle Trunk	muscle
15	chr6:15332000-15359400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:15332800-15341600	Weak transcription	HSMM	muscle
17	chr6:15333000-15341000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr6:15333000-15341600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr6:15333200-15351400	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr6:15333400-15340600	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr6:15333800-15347600	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr6:15334800-15350200	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr6:15335400-15349800	Enhancers	Fetal Thymus	thymus
24	chr6:15335600-15340600	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr6:15336200-15340800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr6:15337000-15340800	Enhancers	K562	blood
27	chr6:15337200-15341000	Weak transcription	Fetal Intestine Large	intestine
28	chr6:15337400-15340600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr6:15337400-15341000	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr6:15337600-15340600	Enhancers	Gastric	stomach
31	chr6:15337600-15340800	Enhancers	Primary T cells from cord blood	blood
32	chr6:15337600-15340800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr6:15337600-15342600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr6:15337800-15340800	Weak transcription	Brain Substantia Nigra	brain
35	chr6:15337800-15341000	Weak transcription	Pancreas	Pancrea
36	chr6:15337800-15346400	Weak transcription	NHDF-Ad	bronchial
37	chr6:15338000-15340800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr6:15338000-15340800	Enhancers	Primary hematopoietic stem cells	blood
39	chr6:15338000-15351600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr6:15338200-15342400	Weak transcription	Brain Angular Gyrus	brain
41	chr6:15338400-15341000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr6:15338400-15342400	Weak transcription	Lung	lung
43	chr6:15338400-15349800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr6:15338400-15351600	Weak transcription	Colon Smooth Muscle	Colon
45	chr6:15338600-15340600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr6:15338600-15341000	Weak transcription	Brain Anterior Caudate	brain
47	chr6:15338600-15343800	Weak transcription	Right Ventricle	heart
48	chr6:15338800-15340600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr6:15338800-15340600	Enhancers	Monocytes-CD14+_RO01746	blood
50	chr6:15338800-15341800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links