Variant report

Variant	rs12199895
Chromosome Location	chr6:15316052-15316053
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:15244134..15247491-chr6:15313536..15316337,3	K562	blood:

Variant related genes	Relation type
ENSG00000008083	Chromatin interaction
ENSG00000271888	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10949291	0.85[ASN][1000 genomes]
rs10949292	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10949293	0.80[ASN][1000 genomes]
rs10949294	1.00[CHB][hapmap]
rs10949295	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs11759040	1.00[JPT][hapmap]
rs11759478	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11759828	0.80[ASN][1000 genomes]
rs11759847	0.80[ASN][1000 genomes]
rs12192599	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12198692	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]
rs12198694	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];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12204124	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs12205420	0.80[ASN][1000 genomes]
rs12206745	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12209228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12209453	0.80[ASN][1000 genomes]
rs12209539	0.85[ASN][1000 genomes]
rs12209748	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12210592	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12211278	1.00[CHB][hapmap]
rs12211777	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12212013	0.90[ASN][1000 genomes]
rs12214719	0.96[EUR][1000 genomes]
rs12215596	0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[ASN][1000 genomes]
rs12215740	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13192347	1.00[CHB][hapmap]
rs13194410	1.00[CHB][hapmap]
rs13205396	1.00[CHB][hapmap]
rs13205612	1.00[CHB][hapmap]
rs16876250	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs16876278	1.00[CHB][hapmap]
rs17575737	1.00[CEU][hapmap];1.00[CHB][hapmap]
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];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17637773	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs17638192	1.00[CHB][hapmap]
rs17687211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17713010	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs55634912	0.90[ASN][1000 genomes]
rs55980198	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6459405	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs6902997	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6903550	0.81[AFR][1000 genomes]
rs6907856	1.00[YRI][hapmap]
rs6919296	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6923291	1.00[YRI][hapmap]
rs6935879	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6938919	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6941561	1.00[YRI][hapmap]
rs72834551	0.85[ASN][1000 genomes]
rs72834590	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7765425	1.00[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.90[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:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15306000-15318600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:15309200-15320600	Weak transcription	A549	lung
3	chr6:15310200-15318200	Weak transcription	Fetal Kidney	kidney
4	chr6:15311000-15322200	Weak transcription	Fetal Intestine Small	intestine
5	chr6:15311200-15317600	Weak transcription	Stomach Mucosa	stomach
6	chr6:15311200-15330600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr6:15312200-15317400	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr6:15312600-15316400	Enhancers	K562	blood
9	chr6:15312600-15317200	Enhancers	Psoas Muscle	Psoas
10	chr6:15312800-15318000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr6:15312800-15318000	Weak transcription	Fetal Muscle Trunk	muscle
12	chr6:15313200-15316400	Weak transcription	HepG2	liver
13	chr6:15313200-15317200	Enhancers	H9 Cell Line	embryonic stem cell
14	chr6:15313200-15317800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr6:15313200-15318000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:15313200-15318400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr6:15313200-15318400	Weak transcription	NHDF-Ad	bronchial
18	chr6:15313200-15320400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:15313200-15322400	Weak transcription	HMEC	breast
20	chr6:15313200-15322800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr6:15313200-15323400	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr6:15313200-15326600	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr6:15313400-15318000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr6:15313400-15318600	Weak transcription	NH-A	brain
25	chr6:15313400-15322600	Weak transcription	Osteobl	bone
26	chr6:15313600-15318400	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr6:15313600-15322800	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr6:15313800-15317800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr6:15313800-15318000	Weak transcription	Fetal Lung	lung
30	chr6:15313800-15318000	Weak transcription	NHLF	lung
31	chr6:15313800-15318600	Weak transcription	HSMM	muscle
32	chr6:15313800-15321000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr6:15313800-15321000	Weak transcription	NHEK	skin
34	chr6:15313800-15321200	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr6:15313800-15325400	Weak transcription	Liver	Liver
36	chr6:15314000-15317800	Weak transcription	Lung	lung
37	chr6:15314000-15318000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr6:15314000-15318000	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr6:15314000-15318200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr6:15314000-15318400	Weak transcription	Stomach Smooth Muscle	stomach
41	chr6:15314000-15318600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr6:15314000-15322000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr6:15314000-15322400	Weak transcription	Gastric	stomach
44	chr6:15314000-15323800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr6:15314200-15317400	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr6:15314200-15317800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr6:15314200-15317800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr6:15314200-15318000	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr6:15314200-15318000	Weak transcription	Fetal Muscle Leg	muscle
50	chr6:15314200-15318200	Weak transcription	Adipose Nuclei	Adipose

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