Variant report

Variant	rs2237150
Chromosome Location	chr6:15408528-15408529
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:15402089..15404212-chr6:15407059..15409660,2	MCF-7	breast:
2	chr6:15390400..15392545-chr6:15407665..15410299,2	MCF-7	breast:
3	chr6:15401226..15405320-chr6:15407295..15410337,3	K562	blood:
4	chr6:15399207..15401117-chr6:15408495..15411359,2	K562	blood:
5	chr6:15209991..15212845-chr6:15406600..15410606,5	K562	blood:

Variant related genes	Relation type
ENSG00000008083	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1474588	0.81[CEU][hapmap]
rs2072819	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs2237121	0.82[GIH][hapmap];0.92[MEX][hapmap]
rs2237124	0.91[MEX][hapmap]
rs2237141	0.82[CEU][hapmap]
rs2237145	0.81[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2237149	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2237152	0.88[CEU][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes]
rs2237153	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2237156	0.96[CEU][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2237157	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs2282821	0.82[CHB][hapmap]
rs2282825	0.91[CHB][hapmap]
rs2282826	0.82[CHB][hapmap]
rs2282827	0.82[CHB][hapmap]
rs2299045	0.81[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap];0.82[ASN][1000 genomes]
rs2299048	0.84[MEX][hapmap]
rs2299053	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2299054	0.96[CEU][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3778652	0.81[CEU][hapmap];0.84[GIH][hapmap];0.80[MKK][hapmap];0.84[TSI][hapmap]
rs4085876	0.81[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];0.84[TSI][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6459406	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7754701	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7754755	0.87[ASN][1000 genomes]
rs9349978	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9358059	0.88[EUR][1000 genomes]
rs9358060	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9370813	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9383051	0.92[CEU][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs9383054	0.96[CEU][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9464785	0.86[EUR][1000 genomes]
rs9464787	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs9476820	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs9476827	0.81[CEU][hapmap];0.84[GIH][hapmap];0.84[TSI][hapmap]

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	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
6	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
7	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
8	nsv1019927	chr6:15351240-15419257	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv538145	chr6:15351240-15419257	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2237150	TDG	trans	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15396200-15410200	Enhancers	HUES64 Cell Line	embryonic stem cell
2	chr6:15399000-15410600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:15400400-15412800	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr6:15400800-15411200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr6:15401200-15414000	Weak transcription	Aorta	Aorta
6	chr6:15401200-15417200	Weak transcription	Lung	lung
7	chr6:15401200-15426200	Weak transcription	Pancreas	Pancrea
8	chr6:15401400-15411600	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr6:15401600-15415800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr6:15402600-15413600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr6:15403000-15409200	Weak transcription	Placenta	Placenta
12	chr6:15403000-15409400	Weak transcription	HepG2	liver
13	chr6:15403000-15413600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr6:15403000-15422000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr6:15403400-15408600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr6:15403600-15411400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr6:15404600-15409600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr6:15404600-15413000	Enhancers	Primary hematopoietic stem cells	blood
19	chr6:15404600-15413400	Weak transcription	Ovary	ovary
20	chr6:15404600-15413400	Weak transcription	Osteobl	bone
21	chr6:15404600-15413600	Weak transcription	NHEK	skin
22	chr6:15404600-15413800	Weak transcription	Esophagus	oesophagus
23	chr6:15404600-15420800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr6:15404600-15421200	Weak transcription	Spleen	Spleen
25	chr6:15404800-15411200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr6:15404800-15412000	Weak transcription	Colon Smooth Muscle	Colon
27	chr6:15404800-15413400	Weak transcription	Fetal Muscle Leg	muscle
28	chr6:15404800-15417800	Weak transcription	NH-A	brain
29	chr6:15404800-15427600	Weak transcription	Stomach Smooth Muscle	stomach
30	chr6:15404800-15429000	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr6:15405000-15409200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr6:15405000-15409600	Weak transcription	Stomach Mucosa	stomach
33	chr6:15405000-15409600	Weak transcription	A549	lung
34	chr6:15405000-15413800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr6:15405200-15409200	Weak transcription	Fetal Intestine Large	intestine
36	chr6:15405200-15410600	Weak transcription	Primary B cells from cord blood	blood
37	chr6:15405200-15410600	Weak transcription	Small Intestine	intestine
38	chr6:15405200-15411600	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr6:15405200-15418600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr6:15405400-15417000	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr6:15405600-15409000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr6:15405600-15409000	Weak transcription	Dnd41	blood
43	chr6:15405600-15409400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr6:15405600-15409800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr6:15405600-15410600	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr6:15405600-15411800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr6:15405600-15413600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr6:15405600-15422000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr6:15405800-15409000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr6:15405800-15409200	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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