Variant report

Variant	rs1553886
Chromosome Location	chr15:83431905-83431906
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83418321..83420816-chr15:83430517..83433004,2	MCF-7	breast:
2	chr15:83417260..83420154-chr15:83431277..83434001,3	MCF-7	breast:
3	chr15:83349269..83350840-chr15:83431347..83434212,2	MCF-7	breast:
4	chr15:83429645..83432307-chr15:83436873..83440129,3	K562	blood:

Variant related genes	Relation type
ENSG00000250988	Chromatin interaction
ENSG00000103723	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1105287	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11631033	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11631209	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11631378	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11633676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11635290	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11635357	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11637448	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11637563	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11857233	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs1256430	0.82[GIH][hapmap]
rs12907810	0.82[CEU][hapmap];0.95[GIH][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs12914752	0.87[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12917248	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2137052	0.90[EUR][1000 genomes]
rs34337936	0.88[EUR][1000 genomes]
rs35590674	0.90[EUR][1000 genomes]
rs35852340	0.91[EUR][1000 genomes]
rs35989107	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35989256	0.90[EUR][1000 genomes]
rs3814281	0.95[GIH][hapmap];0.85[TSI][hapmap]
rs4132210	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4779061	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57252413	0.84[EUR][1000 genomes]
rs60414706	0.84[EUR][1000 genomes]
rs72753973	0.91[EUR][1000 genomes]
rs9806642	0.82[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054171	chr15:83237514-83468077	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1036950	chr15:83245326-83461261	Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Active TSS Enhancers Bivalent/Poised 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	43 gene(s)	inside rSNPs	diseases
3	nsv1036462	chr15:83245326-83472507	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	esv34318	chr15:83283555-83453495	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	esv3493740	chr15:83295897-83458896	Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
6	esv3493739	chr15:83296247-83458846	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
7	esv3493738	chr15:83296905-83457854	Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
8	esv3493742	chr15:83296993-83457792	Weak transcription Active TSS Bivalent Enhancer Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
9	nsv817702	chr15:83299461-83457424	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
10	nsv469557	chr15:83417763-83560629	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
11	nsv482340	chr15:83417763-83560629	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
12	nsv471687	chr15:83417764-83560629	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
13	esv3346074	chr15:83422947-83456222	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1553886	FAM154B	cis	parietal	SCAN
rs1553886	PSMA4	cis	parietal	SCAN
rs1553886	LOC653344	cis	multi-tissue	Pritchard
rs1553886	WHAMM	cis	parietal	SCAN
rs1553886	RASGRF1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83420200-83433400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:83420400-83436400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr15:83421200-83432000	Strong transcription	A549	lung
4	chr15:83421600-83432800	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr15:83422200-83435200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr15:83422400-83436800	Strong transcription	Primary T cells from cord blood	blood
7	chr15:83424000-83432600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:83424200-83432800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr15:83425000-83435400	Weak transcription	Fetal Kidney	kidney
10	chr15:83425000-83447800	Weak transcription	Fetal Brain Male	brain
11	chr15:83425200-83436200	Weak transcription	Colonic Mucosa	Colon
12	chr15:83425600-83435400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr15:83425600-83435400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr15:83426200-83432600	Strong transcription	Left Ventricle	heart
15	chr15:83427000-83432000	Strong transcription	Stomach Smooth Muscle	stomach
16	chr15:83427200-83432400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr15:83427200-83432600	Strong transcription	Fetal Muscle Trunk	muscle
18	chr15:83427600-83432400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr15:83427800-83432200	Weak transcription	Brain Anterior Caudate	brain
20	chr15:83427800-83432600	Weak transcription	Dnd41	blood
21	chr15:83427800-83433800	Weak transcription	Pancreas	Pancrea
22	chr15:83427800-83434000	Weak transcription	Fetal Lung	lung
23	chr15:83427800-83437200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr15:83427800-83442200	Weak transcription	Brain Substantia Nigra	brain
25	chr15:83428000-83432200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr15:83428000-83432400	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr15:83428000-83432600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr15:83428000-83433600	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr15:83428000-83433600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr15:83428000-83433600	Weak transcription	Gastric	stomach
31	chr15:83428000-83433800	Weak transcription	Thymus	Thymus
32	chr15:83428000-83434800	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr15:83428000-83436000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr15:83428000-83436400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr15:83428000-83438200	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr15:83428000-83440400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr15:83428000-83440400	Weak transcription	Esophagus	oesophagus
38	chr15:83428000-83441000	Weak transcription	K562	blood
39	chr15:83428000-83442200	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr15:83428200-83432600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr15:83428200-83432600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr15:83428200-83432800	Weak transcription	HUVEC	blood vessel
43	chr15:83428200-83433400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr15:83428200-83433600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr15:83428200-83433600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr15:83428200-83433600	Weak transcription	Fetal Stomach	stomach
47	chr15:83428200-83433600	Weak transcription	Spleen	Spleen
48	chr15:83428200-83433800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr15:83428200-83433800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr15:83428200-83433800	Weak transcription	Fetal Intestine Small	intestine

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