Variant report

Variant	rs3775236
Chromosome Location	chr4:87667206-87667207
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:87657826..87659557-chr4:87666648..87668755,2	K562	blood:
2	chr4:87666468..87669135-chr4:87669652..87672060,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10003989	0.92[YRI][hapmap];0.86[AFR][1000 genomes]
rs10008165	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs10012566	0.82[AMR][1000 genomes]
rs10016074	0.97[ASN][1000 genomes]
rs10019950	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10023787	0.85[JPT][hapmap]
rs10033679	0.91[YRI][hapmap];0.84[AFR][1000 genomes]
rs1026861	0.82[ASN][1000 genomes]
rs1035191	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10516778	0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs11097118	0.86[YRI][hapmap];0.80[AFR][1000 genomes]
rs11097120	0.82[YRI][hapmap]
rs11930396	0.86[CEU][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12171458	0.82[AMR][1000 genomes]
rs12331502	0.93[ASN][1000 genomes]
rs12503659	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12510802	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13113689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1420621	0.85[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs17012072	0.85[JPT][hapmap]
rs17420607	0.94[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs17420966	0.83[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17453839	0.80[JPT][hapmap]
rs17454154	0.97[ASN][1000 genomes]
rs17454662	0.90[ASN][1000 genomes]
rs17694112	0.85[JPT][hapmap]
rs2006842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2054592	0.85[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2054593	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2230600	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs2287147	0.85[JPT][hapmap]
rs3775238	0.93[ASN][1000 genomes]
rs3775239	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4263359	0.90[ASN][1000 genomes]
rs4693152	0.87[CEU][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs4693780	0.84[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs57954319	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6531932	0.81[JPT][hapmap]
rs67867077	0.91[ASN][1000 genomes]
rs71605615	0.84[AFR][1000 genomes]
rs72665791	0.90[ASN][1000 genomes]
rs7658220	0.82[EUR][1000 genomes]
rs7664147	0.91[YRI][hapmap];0.86[AFR][1000 genomes]
rs7664860	0.91[YRI][hapmap];0.84[AFR][1000 genomes]
rs7688019	0.87[CEU][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs7698481	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs7699564	0.91[YRI][hapmap]
rs9307026	0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs969734	0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs9997453	0.92[YRI][hapmap];0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2757071	chr4:87417291-87689533	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	esv2759264	chr4:87417291-87689533	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	nsv830001	chr4:87585278-87748643	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv508296	chr4:87636350-87667372	ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3775236	PTPN13	cis	brain	BrainEAC
rs3775236	PTPN13	cis	intralobular white matter	BrainEAC

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87631200-87712200	Weak transcription	Aorta	Aorta
2	chr4:87635200-87737400	Weak transcription	Fetal Brain Male	brain
3	chr4:87636400-87683800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr4:87639200-87688000	Weak transcription	Fetal Intestine Large	intestine
5	chr4:87639400-87739200	Weak transcription	A549	lung
6	chr4:87641800-87683400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr4:87642200-87692600	Weak transcription	NH-A	brain
8	chr4:87642400-87735800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr4:87642600-87692400	Weak transcription	Colon Smooth Muscle	Colon
10	chr4:87642600-87697600	Weak transcription	Brain Angular Gyrus	brain
11	chr4:87642600-87719200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr4:87644600-87680600	Weak transcription	NHLF	lung
13	chr4:87650400-87677400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr4:87651800-87676400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr4:87652600-87670000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr4:87655600-87704400	Weak transcription	Hela-S3	cervix
17	chr4:87659000-87676400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr4:87661600-87671600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr4:87661600-87671600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr4:87661600-87680400	Weak transcription	Brain Substantia Nigra	brain
21	chr4:87661600-87680600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr4:87661600-87683200	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr4:87661600-87710200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr4:87661600-87711400	Weak transcription	Brain Germinal Matrix	brain
25	chr4:87661600-87712000	Weak transcription	Esophagus	oesophagus
26	chr4:87661600-87737800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr4:87661800-87670400	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr4:87661800-87671400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr4:87661800-87671600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr4:87661800-87671600	Weak transcription	Lung	lung
31	chr4:87661800-87676600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr4:87661800-87683000	Weak transcription	Fetal Stomach	stomach
33	chr4:87661800-87683200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr4:87661800-87683800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr4:87661800-87708000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr4:87661800-87712000	Weak transcription	Fetal Intestine Small	intestine
37	chr4:87661800-87728800	Weak transcription	Pancreas	Pancrea
38	chr4:87662000-87669000	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr4:87662000-87669200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr4:87662000-87675600	Weak transcription	Gastric	stomach
41	chr4:87662400-87669600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr4:87663000-87672200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr4:87663000-87683600	Weak transcription	Fetal Brain Female	brain
44	chr4:87663000-87711400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr4:87663400-87675400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr4:87664000-87670800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr4:87664400-87667800	Strong transcription	HMEC	breast
48	chr4:87665000-87692400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr4:87665600-87668600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr4:87665600-87669800	Strong transcription	Fetal Lung	lung

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