Variant report

Variant	rs9288967
Chromosome Location	chr3:112717319-112717320
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:112715780..112719383-chr3:112720477..112724820,4	MCF-7	breast:
2	chr3:112716379..112718030-chr3:112718654..112721111,2	K562	blood:
3	chr3:112709443..112715203-chr3:112715449..112720503,7	MCF-7	breast:
4	chr3:112708475..112712814-chr3:112716672..112721404,6	MCF-7	breast:
5	chr3:112713372..112715883-chr3:112716747..112720501,3	MCF-7	breast:
6	chr3:112708277..112711427-chr3:112715953..112720646,6	K562	blood:

Variant related genes	Relation type
ENSG00000163607	Chromatin interaction
ENSG00000272844	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10934211	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11718449	1.00[MEX][hapmap];0.82[TSI][hapmap]
rs1488189	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1488190	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2272393	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2293560	0.96[ASN][1000 genomes]
rs2293562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2306857	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs33940464	0.80[YRI][hapmap]
rs3872610	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.96[ASN][1000 genomes]
rs3889123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4682451	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4682452	1.00[LWK][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs6438123	0.85[CEU][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6796453	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7633507	0.97[ASN][1000 genomes]
rs7650656	0.85[CHB][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap]
rs9866791	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9874803	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	esv1843165	chr3:112628205-112740145	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9288967	GTPBP8	Cis_1M	lymphoblastoid	RTeQTL
rs9288967	GTPBP8	cis	lymphoblastoid	seeQTL
rs9288967	GTPBP8	cis	multi-tissue	Pritchard
rs9288967	C3orf17	cis	cerebellum	SCAN
rs9288967	SIDT1	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112710400-112721200	Weak transcription	Lung	lung
2	chr3:112710400-112721400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:112710400-112721400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:112710400-112724200	Weak transcription	Small Intestine	intestine
5	chr3:112710400-112737400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:112710600-112721000	Weak transcription	Pancreas	Pancrea
7	chr3:112710600-112721000	Weak transcription	Right Ventricle	heart
8	chr3:112710600-112721000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:112710600-112721200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr3:112710600-112721200	Weak transcription	Ovary	ovary
11	chr3:112710600-112721400	Weak transcription	HSMMtube	muscle
12	chr3:112710600-112723800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:112710600-112725000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr3:112710800-112718400	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr3:112710800-112718800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr3:112710800-112721400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr3:112711200-112718600	Weak transcription	Colonic Mucosa	Colon
18	chr3:112711400-112718000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr3:112711400-112718800	Weak transcription	Fetal Stomach	stomach
20	chr3:112711400-112719800	Weak transcription	Brain Substantia Nigra	brain
21	chr3:112711400-112721200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr3:112711400-112721200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr3:112711400-112721200	Weak transcription	Psoas Muscle	Psoas
24	chr3:112711400-112721200	Weak transcription	Spleen	Spleen
25	chr3:112711400-112736600	Weak transcription	Stomach Mucosa	stomach
26	chr3:112711600-112717400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr3:112711600-112718600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr3:112711600-112718600	Weak transcription	NHDF-Ad	bronchial
29	chr3:112711600-112718800	Weak transcription	Fetal Intestine Small	intestine
30	chr3:112711600-112720200	Weak transcription	K562	blood
31	chr3:112711600-112721000	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr3:112711600-112721000	Weak transcription	Rectal Smooth Muscle	rectum
33	chr3:112711600-112721200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr3:112711800-112721200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr3:112711800-112724000	Weak transcription	NHLF	lung
36	chr3:112712000-112718600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr3:112712000-112721200	Weak transcription	Brain Hippocampus Middle	brain
38	chr3:112712000-112721400	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr3:112712200-112719600	Weak transcription	Hela-S3	cervix
40	chr3:112712200-112736800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:112712400-112717400	Weak transcription	Fetal Kidney	kidney
42	chr3:112712400-112736600	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr3:112712800-112718400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr3:112712800-112719800	Weak transcription	Brain Anterior Caudate	brain
45	chr3:112712800-112721200	Weak transcription	Aorta	Aorta
46	chr3:112712800-112721400	Weak transcription	Fetal Brain Male	brain
47	chr3:112712800-112736600	Weak transcription	Fetal Heart	heart
48	chr3:112713200-112718600	Weak transcription	Brain Angular Gyrus	brain
49	chr3:112714000-112719400	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr3:112714400-112721000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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