Variant report

Variant	rs6496874
Chromosome Location	chr15:92475343-92475344
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:92474072..92476902-chr15:92480050..92482892,3	MCF-7	breast:
2	chr15:92470402..92472292-chr15:92475155..92476710,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10775254	0.87[ASN][1000 genomes]
rs11074026	0.81[ASN][1000 genomes]
rs12591949	0.84[ASN][1000 genomes]
rs12594572	0.84[EUR][1000 genomes]
rs3924427	0.84[ASN][1000 genomes]
rs4077721	0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4244910	0.88[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap];0.93[ASN][1000 genomes]
rs4294800	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4520813	0.91[ASN][1000 genomes]
rs6496868	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6496870	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6496872	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6496873	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6496875	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6496876	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6496877	0.81[JPT][hapmap]
rs6496878	0.81[JPT][hapmap]
rs7162293	0.87[ASN][1000 genomes]
rs7163871	0.81[CEU][hapmap]
rs7174549	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7179389	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7179958	0.81[JPT][hapmap]
rs7181500	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7182106	0.87[ASN][1000 genomes]
rs8035875	0.87[ASN][1000 genomes]
rs8041346	0.87[ASN][1000 genomes]
rs9920349	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048635	chr15:92073294-92557339	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv870094	chr15:92367354-92631647	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv534110	chr15:92397220-92592961	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6496874	SERPINB9	trans	parietal	SCAN
rs6496874	FAM174B	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:92462800-92482600	Weak transcription	HMEC	breast
2	chr15:92463800-92482400	Weak transcription	Esophagus	oesophagus
3	chr15:92464600-92483000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr15:92466400-92482200	Weak transcription	Pancreas	Pancrea
5	chr15:92466800-92480200	Weak transcription	Fetal Brain Female	brain
6	chr15:92468000-92478800	Weak transcription	Lung	lung
7	chr15:92469200-92477400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr15:92469400-92483000	Weak transcription	Gastric	stomach
9	chr15:92469400-92485800	Weak transcription	Aorta	Aorta
10	chr15:92469600-92477200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr15:92470200-92478000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr15:92470200-92478600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr15:92470400-92483200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr15:92470600-92479800	Weak transcription	NHLF	lung
15	chr15:92470800-92478400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr15:92471000-92477200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr15:92471000-92478400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr15:92471200-92483600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr15:92471800-92481400	Weak transcription	Brain Anterior Caudate	brain
20	chr15:92472400-92475600	Enhancers	Fetal Heart	heart
21	chr15:92472600-92475600	Weak transcription	Right Atrium	heart
22	chr15:92472600-92479200	Weak transcription	Ovary	ovary
23	chr15:92472800-92478600	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr15:92472800-92482400	Weak transcription	Spleen	Spleen
25	chr15:92473200-92478400	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr15:92473600-92476400	Weak transcription	Left Ventricle	heart
27	chr15:92473600-92479800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr15:92473600-92483200	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr15:92474000-92475400	Enhancers	H1 Cell Line	embryonic stem cell
30	chr15:92474200-92475400	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr15:92474200-92475400	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr15:92474200-92475400	Enhancers	Brain Hippocampus Middle	brain
33	chr15:92474400-92475400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr15:92474400-92475400	Enhancers	Brain Cingulate Gyrus	brain
35	chr15:92474400-92475800	Enhancers	Brain Substantia Nigra	brain
36	chr15:92474400-92476200	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr15:92474600-92478800	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr15:92474800-92478800	Weak transcription	Right Ventricle	heart
39	chr15:92475000-92475400	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr15:92475000-92478600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr15:92475200-92475400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr15:92475200-92475400	Enhancers	Primary T cells from cord blood	blood
43	chr15:92475200-92475600	Enhancers	Pancreatic Islets	Pancreatic Islet
44	chr15:92475200-92479600	Weak transcription	Fetal Brain Male	brain
45	chr15:92475200-92479800	Weak transcription	Brain Angular Gyrus	brain
46	chr15:92475200-92480200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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