Variant report

Variant	rs11930396
Chromosome Location	chr4:87731238-87731239
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	chr4:87726325..87728258-chr4:87729509..87731494,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10000226	0.90[AFR][1000 genomes]
rs10012566	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10019950	0.82[EUR][1000 genomes]
rs1035191	0.86[CEU][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs10516778	0.85[JPT][hapmap]
rs11561681	0.86[ASN][1000 genomes]
rs12171458	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12503659	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12510802	0.82[EUR][1000 genomes]
rs13113689	0.85[CEU][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes]
rs1420621	0.85[JPT][hapmap]
rs17012072	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs17420607	0.85[JPT][hapmap]
rs17420966	0.86[JPT][hapmap]
rs17694112	0.90[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.91[ASN][1000 genomes]
rs2006842	0.88[ASW][hapmap];0.86[CEU][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2054592	0.85[JPT][hapmap]
rs2054593	0.86[CEU][hapmap];0.81[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs2287147	0.90[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.95[ASN][1000 genomes]
rs3775236	0.86[CEU][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3775239	0.94[ASW][hapmap];0.82[CEU][hapmap];0.81[CHB][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes]
rs4693152	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4693780	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs4693784	0.94[ASN][1000 genomes]
rs55670248	0.94[ASN][1000 genomes]
rs6817630	0.91[YRI][hapmap]
rs72665795	0.94[ASN][1000 genomes]
rs7658220	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7688019	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9307026	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs969734	0.85[JPT][hapmap];0.80[MEX][hapmap]
rs9985645	1.00[YRI][hapmap];0.89[AFR][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	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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11930396	PTPN13	cis	parietal	SCAN
rs11930396	PTPN13	cis	cerebellum	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87635200-87737400	Weak transcription	Fetal Brain Male	brain
2	chr4:87639400-87739200	Weak transcription	A549	lung
3	chr4:87642400-87735800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr4:87661600-87737800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:87689400-87738200	Weak transcription	Gastric	stomach
6	chr4:87690000-87738800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr4:87690800-87736000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr4:87692800-87734200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr4:87694400-87735600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr4:87696800-87733600	Weak transcription	NHLF	lung
11	chr4:87698600-87738600	Weak transcription	Brain Angular Gyrus	brain
12	chr4:87712000-87736600	Weak transcription	Fetal Muscle Trunk	muscle
13	chr4:87712600-87733600	Weak transcription	Lung	lung
14	chr4:87712600-87735800	Weak transcription	Brain Germinal Matrix	brain
15	chr4:87712600-87737600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr4:87712600-87738400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr4:87712600-87751400	Weak transcription	Aorta	Aorta
18	chr4:87712800-87732000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr4:87712800-87736400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr4:87712800-87737000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr4:87712800-87739600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr4:87714400-87731800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr4:87715600-87732600	Weak transcription	Brain Substantia Nigra	brain
24	chr4:87715800-87737400	Weak transcription	Colon Smooth Muscle	Colon
25	chr4:87717200-87737000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr4:87717800-87732400	Weak transcription	Fetal Thymus	thymus
27	chr4:87718000-87732400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr4:87719200-87738600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr4:87719400-87738000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr4:87720000-87736200	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr4:87720800-87732200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr4:87721800-87733600	Weak transcription	Fetal Stomach	stomach
33	chr4:87722600-87736400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr4:87723800-87736200	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr4:87723800-87736200	Weak transcription	Fetal Brain Female	brain
36	chr4:87724000-87737000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr4:87724600-87737600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr4:87724800-87734400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr4:87724800-87736400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr4:87725000-87734000	Strong transcription	NHDF-Ad	bronchial
41	chr4:87725800-87733200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr4:87725800-87739200	Weak transcription	Hela-S3	cervix
43	chr4:87726600-87735600	Weak transcription	NH-A	brain
44	chr4:87727200-87736400	Weak transcription	Left Ventricle	heart
45	chr4:87727600-87733200	Strong transcription	Fetal Kidney	kidney
46	chr4:87727800-87737200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr4:87728200-87736200	Weak transcription	Fetal Intestine Small	intestine
48	chr4:87728400-87736400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr4:87728600-87731400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr4:87728600-87731400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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