Variant report

Variant	rs9993042
Chromosome Location	chr4:87530343-87530344
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:87530294..87531963-chr4:87533296..87535743,2	K562	blood:
2	chr4:87526249..87528781-chr4:87528891..87530850,2	MCF-7	breast:

Extended variants
information (count: 128 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10008165	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10023787	0.90[CEU][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10029671	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs10030525	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10031843	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1021101	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1026861	0.90[CEU][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1035191	0.80[GIH][hapmap]
rs10516778	0.87[GIH][hapmap];0.80[JPT][hapmap]
rs11097115	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11943428	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11947018	0.90[CEU][hapmap];0.83[CHB][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11947775	0.80[ASN][1000 genomes]
rs1420621	0.85[CEU][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs1481833	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17011986	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17418801	0.81[ASN][1000 genomes]
rs17418878	0.81[ASN][1000 genomes]
rs17419295	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs17419627	0.89[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17419929	0.89[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.88[ASN][1000 genomes]
rs17420607	0.81[CHD][hapmap];0.87[GIH][hapmap];0.80[JPT][hapmap]
rs17452556	0.81[ASN][1000 genomes]
rs17453839	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2006842	0.80[GIH][hapmap]
rs2054592	0.80[JPT][hapmap]
rs28483710	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28485273	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs28529445	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28534599	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28535527	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs28663376	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28678816	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28735881	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3775239	0.80[GIH][hapmap]
rs4235081	0.82[ASN][1000 genomes]
rs4277747	0.92[ASN][1000 genomes]
rs4405982	0.84[ASN][1000 genomes]
rs4407468	0.84[ASN][1000 genomes]
rs4452393	0.85[ASN][1000 genomes]
rs4466012	0.84[ASN][1000 genomes]
rs4511966	0.85[ASN][1000 genomes]
rs4513526	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4529013	0.89[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs4552430	0.82[ASN][1000 genomes]
rs4607180	0.84[ASN][1000 genomes]
rs4622964	0.84[ASN][1000 genomes]
rs4640633	0.80[ASN][1000 genomes]
rs4693147	0.94[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs4693772	0.80[ASN][1000 genomes]
rs4693776	0.84[ASN][1000 genomes]
rs4693777	0.82[ASN][1000 genomes]
rs4693780	0.87[GIH][hapmap];0.80[JPT][hapmap]
rs55640323	0.92[ASN][1000 genomes]
rs55653332	0.80[ASN][1000 genomes]
rs55654230	0.94[ASN][1000 genomes]
rs55660529	0.81[ASN][1000 genomes]
rs55722156	0.81[ASN][1000 genomes]
rs55746316	0.97[ASN][1000 genomes]
rs55757426	0.97[ASN][1000 genomes]
rs55773619	0.97[ASN][1000 genomes]
rs55842318	0.84[ASN][1000 genomes]
rs55872468	0.84[ASN][1000 genomes]
rs55879246	0.97[ASN][1000 genomes]
rs55908925	0.84[ASN][1000 genomes]
rs55930543	0.84[ASN][1000 genomes]
rs55978957	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs55982489	0.84[ASN][1000 genomes]
rs56009992	0.84[ASN][1000 genomes]
rs56150118	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56164000	0.82[ASN][1000 genomes]
rs56178389	0.95[ASN][1000 genomes]
rs56222033	0.81[ASN][1000 genomes]
rs56296936	0.97[ASN][1000 genomes]
rs56348925	0.95[ASN][1000 genomes]
rs56353461	0.82[ASN][1000 genomes]
rs59644743	0.82[ASN][1000 genomes]
rs61152200	0.84[ASN][1000 genomes]
rs6531932	0.90[CEU][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66669421	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs67274037	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs67341369	0.92[ASN][1000 genomes]
rs67523832	0.94[ASN][1000 genomes]
rs67928053	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6822396	0.89[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]
rs6838659	0.89[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs6847139	0.89[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs72665711	0.80[ASN][1000 genomes]
rs72665712	0.80[ASN][1000 genomes]
rs72665714	0.80[ASN][1000 genomes]
rs72665719	0.80[ASN][1000 genomes]
rs72665722	0.83[ASN][1000 genomes]
rs72665724	0.82[ASN][1000 genomes]
rs72665725	0.83[ASN][1000 genomes]
rs72665729	0.84[ASN][1000 genomes]
rs72665734	0.84[ASN][1000 genomes]
rs72665736	0.84[ASN][1000 genomes]
rs72665737	0.84[ASN][1000 genomes]
rs72665738	0.84[ASN][1000 genomes]
rs72665740	0.82[ASN][1000 genomes]
rs72665744	0.84[ASN][1000 genomes]
rs72665746	0.82[ASN][1000 genomes]
rs72665752	0.84[ASN][1000 genomes]
rs72665753	0.85[ASN][1000 genomes]
rs72665756	0.85[ASN][1000 genomes]
rs72665759	0.95[ASN][1000 genomes]
rs72665762	0.95[ASN][1000 genomes]
rs72665769	0.94[ASN][1000 genomes]
rs72665771	0.97[ASN][1000 genomes]
rs72665772	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72665777	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7435744	0.85[ASN][1000 genomes]
rs7673698	0.80[ASN][1000 genomes]
rs7694723	0.94[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs7695011	0.80[ASN][1000 genomes]
rs9307020	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9683663	0.81[ASN][1000 genomes]
rs969734	0.83[GIH][hapmap];0.80[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594786	chr4:87076360-87609320	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
2	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
3	nsv1012836	chr4:87279206-87643558	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv879522	chr4:87473776-87644842	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv822635	chr4:87479576-87622176	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv879523	chr4:87517609-87594472	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv879524	chr4:87517609-87603929	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv968065	chr4:87528229-87536585	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9993042	PTPN13	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87517000-87536600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:87521400-87532800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr4:87521400-87546800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr4:87521800-87535200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr4:87521800-87536000	Weak transcription	Fetal Kidney	kidney
6	chr4:87524200-87531800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr4:87524200-87540800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr4:87525600-87540200	Weak transcription	NHEK	skin
9	chr4:87525800-87532600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr4:87526200-87531800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr4:87526600-87531000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr4:87526600-87532000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr4:87526600-87532600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr4:87526600-87537400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr4:87529000-87532200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr4:87529000-87532400	Weak transcription	Brain Angular Gyrus	brain
17	chr4:87529200-87531000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr4:87529600-87530600	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr4:87529800-87530400	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr4:87529800-87530400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr4:87529800-87531000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr4:87530000-87530400	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr4:87530000-87530400	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr4:87530000-87530400	Enhancers	Brain Cingulate Gyrus	brain
25	chr4:87530000-87532600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr4:87530200-87530600	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr4:87530200-87531600	Weak transcription	Brain Hippocampus Middle	brain
28	chr4:87530200-87531600	Weak transcription	Brain Substantia Nigra	brain
29	chr4:87530200-87532000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr4:87530200-87532200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr4:87530200-87532400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr4:87530200-87532600	Weak transcription	Brain Anterior Caudate	brain

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