Variant report

Variant	rs12198694
Chromosome Location	chr6:15310397-15310398
allele	G/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	EP300	chr6:15309886-15310800	SK-N-SH	brain:	n/a	chr6:15310060-15310074
2	GATA2	chr6:15310017-15310482	SH-SY5Y	brain:	n/a	chr6:15310134-15310150 chr6:15310131-15310138 chr6:15310126-15310142 chr6:15310131-15310141 chr6:15310131-15310152 chr6:15310129-15310139 chr6:15310129-15310138 chr6:15310138-15310147
3	POLR2A	chr6:15310135-15310940	H1-hESC	embryonic stem cell:	n/a	n/a
4	GATA3	chr6:15310263-15310654	SH-SY5Y	brain:	n/a	n/a
5	EP300	chr6:15310199-15310442	SK-N-SH_RA	brain:	n/a	n/a
6	EP300	chr6:15310115-15310573	SK-N-SH_RA	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:15300692..15302915-chr6:15309585..15311589,2	MCF-7	breast:
2	chr6:15309030..15310974-chr6:15337189..15339265,2	K562	blood:

Variant related genes	Relation type
RNU6-522P	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10949291	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10949292	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10949293	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10949294	1.00[CHB][hapmap]
rs10949295	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11759040	1.00[JPT][hapmap]
rs11759478	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11759828	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11759847	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12192599	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12198692	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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12201889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12204124	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12205420	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12206745	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12209228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12209453	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12209539	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12209748	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12210592	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211278	1.00[CHB][hapmap]
rs12211777	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12212013	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12214719	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12215596	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12215740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13192347	1.00[CHB][hapmap]
rs13194410	1.00[CHB][hapmap]
rs13205396	1.00[CHB][hapmap]
rs13205612	1.00[CHB][hapmap]
rs16876250	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16876278	1.00[CHB][hapmap]
rs17575737	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes]
rs17576233	1.00[CHB][hapmap]
rs17576436	1.00[CHB][hapmap]
rs17619730	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs17619838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17637773	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17638192	1.00[CHB][hapmap]
rs17687211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17713010	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55634912	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55980198	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6902997	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6919296	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6935879	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6938919	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72834551	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72834590	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7765425	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15295800-15311400	Enhancers	Primary hematopoietic stem cells	blood
2	chr6:15300200-15312400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr6:15300400-15312600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr6:15300800-15310600	Weak transcription	HSMM	muscle
5	chr6:15301200-15312400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr6:15301200-15313000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr6:15301200-15313400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr6:15303400-15311400	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr6:15303400-15311400	Enhancers	Primary B cells from peripheral blood	blood
10	chr6:15303800-15310600	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr6:15303800-15312600	Weak transcription	Lung	lung
12	chr6:15305200-15311000	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr6:15305200-15313600	Weak transcription	Liver	Liver
14	chr6:15305400-15312600	Weak transcription	Fetal Brain Male	brain
15	chr6:15305600-15310600	Weak transcription	Gastric	stomach
16	chr6:15305600-15312600	Weak transcription	Fetal Brain Female	brain
17	chr6:15305800-15310600	Weak transcription	Esophagus	oesophagus
18	chr6:15306000-15311800	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr6:15306000-15318600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:15306400-15310600	Weak transcription	Fetal Heart	heart
21	chr6:15306400-15312600	Weak transcription	Spleen	Spleen
22	chr6:15306600-15312400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr6:15306600-15313000	Weak transcription	Fetal Muscle Leg	muscle
24	chr6:15307000-15314800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr6:15307400-15311000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:15307400-15311000	Enhancers	Brain Anterior Caudate	brain
27	chr6:15307400-15314400	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr6:15307600-15310400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr6:15307600-15310600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr6:15307600-15310600	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr6:15307600-15311000	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr6:15307600-15311200	Enhancers	Brain Cingulate Gyrus	brain
33	chr6:15307600-15311400	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr6:15307600-15311600	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr6:15307600-15314000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr6:15307800-15310600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr6:15307800-15311000	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr6:15308000-15310400	Enhancers	Primary T cells from cord blood	blood
39	chr6:15308200-15310600	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr6:15308200-15311400	Enhancers	Adipose Nuclei	Adipose
41	chr6:15308200-15311600	Enhancers	Brain Hippocampus Middle	brain
42	chr6:15308200-15312600	Weak transcription	Thymus	Thymus
43	chr6:15308400-15311600	Enhancers	NHDF-Ad	bronchial
44	chr6:15308800-15310800	Enhancers	K562	blood
45	chr6:15308800-15311000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr6:15308800-15311600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr6:15308800-15314800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr6:15309000-15310600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr6:15309000-15310800	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr6:15309000-15310800	Enhancers	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links