Variant report

Variant	rs2040906
Chromosome Location	chr7:149538150-149538151
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:149535432..149538355-chr7:150102358..150106003,3	MCF-7	breast:
2	chr7:149470907..149472534-chr7:149538103..149539944,2	MCF-7	breast:
3	chr7:149535857..149538432-chr7:149551451..149554289,3	MCF-7	breast:
4	chr7:149534427..149538606-chr7:149567610..149571411,8	MCF-7	breast:
5	chr7:149417465..149419893-chr7:149536657..149538216,2	K562	blood:
6	chr7:149520043..149524365-chr7:149535249..149538309,4	MCF-7	breast:
7	chr7:149534468..149539239-chr7:149549126..149555518,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197558	Chromatin interaction
ENSG00000196456	Chromatin interaction
ENSG00000133619	Chromatin interaction
ENSG00000106479	Chromatin interaction
ENSG00000204934	Chromatin interaction
ENSG00000171130	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1005603	1.00[CHB][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs1008336	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs10250401	0.92[ASN][1000 genomes]
rs10252161	0.86[CHB][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs10261977	1.00[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs10262226	0.97[ASN][1000 genomes]
rs1044805	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11979187	1.00[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs12666932	0.83[ASN][1000 genomes]
rs12673475	0.92[ASN][1000 genomes]
rs1557955	0.92[ASN][1000 genomes]
rs1557956	0.92[ASN][1000 genomes]
rs3088250	0.85[YRI][hapmap]
rs4389841	0.93[ASN][1000 genomes]
rs57009176	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57307418	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57339339	0.82[ASN][1000 genomes]
rs62617122	0.96[ASN][1000 genomes]
rs6953743	0.84[ASN][1000 genomes]
rs6958235	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6960187	0.88[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6974897	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6975030	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7791767	1.00[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs7795784	0.84[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034350	chr7:149264094-149666356	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv539190	chr7:149264094-149666356	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1023901	chr7:149364044-149747442	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv539191	chr7:149364044-149747442	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv469576	chr7:149379626-149563233	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv1031581	chr7:149386249-149570178	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv539192	chr7:149386249-149570178	Genic enhancers Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv831184	chr7:149424835-149600093	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	esv2758139	chr7:149441590-149956415	Strong transcription Active TSS Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
10	esv2759571	chr7:149441590-149956415	Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
11	nsv889408	chr7:149458623-149539138	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
12	nsv521861	chr7:149458623-149582906	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
13	nsv889409	chr7:149458623-149585379	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
14	nsv889411	chr7:149465674-149539138	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv1029471	chr7:149496177-149810381	Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
16	nsv539193	chr7:149496177-149810381	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
17	nsv1033095	chr7:149508083-149781872	Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
18	nsv608987	chr7:149509981-149547703	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2040906	SNORD15B	trans	cerebellum	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:149536400-149538400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
2	chr7:149536400-149539600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr7:149536400-149541400	Weak transcription	Lung	lung
4	chr7:149536400-149542600	Weak transcription	Aorta	Aorta
5	chr7:149536400-149543000	Weak transcription	Ovary	ovary
6	chr7:149536400-149543400	Weak transcription	Placenta	Placenta
7	chr7:149536400-149543800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr7:149536400-149544800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr7:149536400-149544800	Weak transcription	Spleen	Spleen
10	chr7:149536400-149547000	Weak transcription	Esophagus	oesophagus
11	chr7:149536400-149556400	Weak transcription	Colonic Mucosa	Colon
12	chr7:149536600-149541400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr7:149536600-149541600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr7:149536600-149541600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr7:149536600-149542000	Weak transcription	Fetal Muscle Trunk	muscle
16	chr7:149536600-149542800	Weak transcription	Primary B cells from cord blood	blood
17	chr7:149536600-149551600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr7:149536800-149538600	Weak transcription	Psoas Muscle	Psoas
19	chr7:149536800-149539400	Weak transcription	Fetal Brain Female	brain
20	chr7:149536800-149541600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr7:149536800-149541800	Weak transcription	Fetal Stomach	stomach
22	chr7:149536800-149541800	Weak transcription	Stomach Smooth Muscle	stomach
23	chr7:149536800-149542000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr7:149536800-149542000	Weak transcription	Brain Germinal Matrix	brain
25	chr7:149536800-149542000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr7:149536800-149542200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr7:149536800-149542400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr7:149536800-149544600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr7:149536800-149544800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr7:149536800-149544800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr7:149536800-149545000	Weak transcription	Duodenum Mucosa	Duodenum
32	chr7:149536800-149545000	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr7:149536800-149551400	Weak transcription	HSMMtube	muscle
34	chr7:149536800-149556400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr7:149537000-149538200	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr7:149537000-149539200	Weak transcription	Brain Angular Gyrus	brain
37	chr7:149537000-149539200	Weak transcription	Fetal Heart	heart
38	chr7:149537000-149539600	Weak transcription	Left Ventricle	heart
39	chr7:149537000-149539600	Weak transcription	Pancreas	Pancrea
40	chr7:149537000-149541000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr7:149537000-149541200	Weak transcription	Fetal Muscle Leg	muscle
42	chr7:149537000-149541400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr7:149537000-149541600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr7:149537000-149541800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr7:149537000-149541800	Weak transcription	Brain Hippocampus Middle	brain
46	chr7:149537000-149541800	Weak transcription	Right Ventricle	heart
47	chr7:149537000-149541800	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr7:149537000-149542000	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr7:149537000-149542000	Weak transcription	Colon Smooth Muscle	Colon
50	chr7:149537000-149542200	Weak transcription	Cortex derived primary cultured neurospheres	brain

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