Variant report

Variant	rs12950225
Chromosome Location	chr17:46145200-46145201
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46143868..46147268-chr17:46149730..46155245,6	K562	blood:
2	chr17:46143868..46147268-chr17:46149730..46152129,3	K562	blood:
3	chr17:46138737..46141088-chr17:46142783..46146686,3	K562	blood:
4	chr17:46139828..46141831-chr17:46142959..46145803,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12603115	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs12603380	0.82[EUR][1000 genomes]
rs12947089	0.87[CEU][hapmap];0.80[CHB][hapmap];0.88[CHD][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap]
rs1316657	0.87[CEU][hapmap];0.80[CHB][hapmap];0.88[CHD][hapmap];0.89[TSI][hapmap]
rs1452666	0.86[CEU][hapmap];0.80[CHB][hapmap]
rs1452667	0.86[CEU][hapmap];0.80[CHB][hapmap]
rs17620033	0.87[CEU][hapmap];0.80[CHB][hapmap];0.88[CHD][hapmap];0.89[TSI][hapmap]
rs1860862	0.87[CEU][hapmap];0.80[CHB][hapmap];0.88[CHD][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap]
rs2021752	0.87[CEU][hapmap];0.80[CHB][hapmap];0.88[CHD][hapmap];0.89[TSI][hapmap]
rs2041572	0.87[CEU][hapmap];0.80[CHB][hapmap]
rs2060876	0.86[CEU][hapmap];0.80[CHB][hapmap]
rs2072441	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2109982	0.87[CEU][hapmap];0.80[CHB][hapmap]
rs2123341	0.87[CEU][hapmap];0.80[CHB][hapmap];0.88[CHD][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap]
rs2278868	0.87[CEU][hapmap];0.80[CHB][hapmap];0.88[CHD][hapmap];0.89[TSI][hapmap]
rs2305433	0.87[CEU][hapmap];0.80[CHB][hapmap];0.86[CHD][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap]
rs2924257	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs3792692	0.87[CEU][hapmap];0.80[CHB][hapmap];0.88[CHD][hapmap];0.89[TSI][hapmap]
rs3792694	0.87[CEU][hapmap];0.80[CHB][hapmap];0.88[CHD][hapmap];0.89[TSI][hapmap]
rs3805370	0.86[CEU][hapmap]
rs3897986	0.87[CEU][hapmap];0.80[CHB][hapmap];0.88[CHD][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap]
rs4793779	0.87[CEU][hapmap];0.85[CHB][hapmap]
rs4794447	0.85[CHB][hapmap]
rs6504108	0.80[CHB][hapmap];0.86[CHD][hapmap]
rs7220768	0.83[CEU][hapmap];0.80[CHB][hapmap];0.88[CHD][hapmap];0.89[TSI][hapmap]
rs7223867	0.87[CEU][hapmap];0.80[CHB][hapmap]
rs7225550	0.87[CEU][hapmap];0.80[CHB][hapmap]
rs758999	0.87[CEU][hapmap];0.80[CHB][hapmap]
rs8069263	0.87[CEU][hapmap];0.80[CHB][hapmap]
rs8072282	0.87[CEU][hapmap];0.80[CHB][hapmap];0.88[CHD][hapmap];0.89[TSI][hapmap]

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	nsv469808	chr17:46049868-46228673	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv482897	chr17:46049868-46228673	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
3	esv1804681	chr17:46144628-46168544	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12950225	SNX11	cis	multi-tissue	Pritchard
rs12950225	CBX1	cis	cerebellum	SCAN
rs12950225	SNX11	cis	parietal	SCAN
rs12950225	HOXB2	cis	multi-tissue	Pritchard
rs12950225	PNPO	cis	parietal	SCAN
rs12950225	SNX11	cis	Lymphoblastoid	GTEx

Chromatin state (count:130 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46130400-46154600	Strong transcription	Primary T cells from cord blood	blood
2	chr17:46130600-46149800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr17:46131200-46154200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr17:46131400-46151000	Strong transcription	Thymus	Thymus
5	chr17:46131400-46154400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr17:46131400-46154400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr17:46132600-46148000	Strong transcription	Primary hematopoietic stem cells	blood
8	chr17:46132600-46155200	Strong transcription	Fetal Thymus	thymus
9	chr17:46132800-46145600	Strong transcription	Fetal Intestine Small	intestine
10	chr17:46133000-46145600	Strong transcription	Fetal Intestine Large	intestine
11	chr17:46133000-46154600	Strong transcription	Fetal Brain Female	brain
12	chr17:46133000-46155200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr17:46133200-46149400	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr17:46133200-46157200	Strong transcription	Fetal Stomach	stomach
15	chr17:46133400-46149800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr17:46133400-46150600	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr17:46133400-46151000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr17:46133400-46154400	Strong transcription	Brain Germinal Matrix	brain
19	chr17:46133400-46154400	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr17:46133400-46154600	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr17:46133400-46155200	Strong transcription	Dnd41	blood
22	chr17:46133600-46149400	Strong transcription	Duodenum Mucosa	Duodenum
23	chr17:46133600-46151400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr17:46133600-46154400	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr17:46133600-46154400	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr17:46133600-46154600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr17:46134000-46146600	Strong transcription	Primary B cells from cord blood	blood
28	chr17:46134000-46154200	Strong transcription	Stomach Smooth Muscle	stomach
29	chr17:46134200-46146000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr17:46134400-46154400	Strong transcription	Primary B cells from peripheral blood	blood
31	chr17:46135400-46155400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr17:46137400-46155200	Strong transcription	Fetal Muscle Trunk	muscle
33	chr17:46137800-46151600	Weak transcription	Stomach Mucosa	stomach
34	chr17:46137800-46154600	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr17:46138000-46154400	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr17:46139000-46145600	Strong transcription	NH-A	brain
37	chr17:46139200-46147200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr17:46139200-46162600	Weak transcription	Small Intestine	intestine
39	chr17:46139800-46162600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr17:46139800-46163600	Weak transcription	Esophagus	oesophagus
41	chr17:46140000-46145800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr17:46140000-46153800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr17:46140000-46162400	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr17:46140200-46156400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr17:46140800-46163200	Weak transcription	Colonic Mucosa	Colon
46	chr17:46141000-46145800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr17:46141800-46145800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr17:46141800-46148600	Weak transcription	Pancreas	Pancrea
49	chr17:46142000-46146200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr17:46142200-46145800	Weak transcription	Brain Angular Gyrus	brain

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