Variant report

Variant	rs3087403
Chromosome Location	chr2:100058870-100058871
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	chr2:100055571..100061199-chr2:100104819..100108042,8	MCF-7	breast:
2	chr2:99950527..99953056-chr2:100056612..100059511,2	K562	blood:

Variant related genes	Relation type
ENSG00000115514	Chromatin interaction
ENSG00000135945	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10496336	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11885942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11887935	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11893359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11896520	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12466114	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12474305	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12479064	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1823569	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1922624	1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs2141907	0.85[EUR][1000 genomes]
rs2305352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2309618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28369945	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28369960	0.83[ASN][1000 genomes]
rs28382977	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3792143	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4341989	0.93[ASW][hapmap];0.95[CEU][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4851203	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4851207	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4851210	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4851212	0.84[GIH][hapmap]
rs61436115	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62153852	0.84[EUR][1000 genomes]
rs62155769	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62155807	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6714650	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6715321	1.00[ASW][hapmap]
rs6748200	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs737094	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][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	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1014604	chr2:99980851-100097884	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1006625	chr2:99984550-100096371	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv1014161	chr2:100021040-100063406	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv962113	chr2:100022168-100317461	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs3087403	ANKRD39	cis	cerebellum	SCAN
rs3087403	TSGA10	cis	multi-tissue	Pritchard
rs3087403	TSGA10	cis	cerebellum	SCAN
rs3087403	LIPT1	cis	cerebellum	SCAN
rs3087403	FAHD2B	cis	parietal	SCAN
rs3087403	LOC129530	cis	multi-tissue	Pritchard
rs3087403	TSGA10	cis	Skin Sun Exposed Lower leg	GTEx
rs3087403	TSGA10	cis	parietal	SCAN
rs3087403	LIPT1	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100005800-100062600	Strong transcription	Dnd41	blood
2	chr2:100005800-100066000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:100006000-100081200	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr2:100021200-100077800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:100022200-100059000	Strong transcription	Liver	Liver
6	chr2:100032600-100078000	Weak transcription	Psoas Muscle	Psoas
7	chr2:100034200-100088800	Weak transcription	Small Intestine	intestine
8	chr2:100036800-100074800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr2:100038200-100063200	Weak transcription	Fetal Intestine Small	intestine
10	chr2:100038200-100073800	Weak transcription	Esophagus	oesophagus
11	chr2:100041400-100077800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr2:100041600-100083400	Weak transcription	Brain Substantia Nigra	brain
13	chr2:100042800-100065000	Weak transcription	Lung	lung
14	chr2:100045000-100064200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr2:100045400-100068200	Weak transcription	Ovary	ovary
16	chr2:100047800-100063200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr2:100048200-100090600	Weak transcription	Stomach Mucosa	stomach
18	chr2:100048400-100067800	Weak transcription	Fetal Heart	heart
19	chr2:100048600-100064000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr2:100048600-100068200	Weak transcription	Spleen	Spleen
21	chr2:100048800-100070400	Weak transcription	Fetal Brain Female	brain
22	chr2:100050000-100065000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr2:100051800-100064600	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr2:100052600-100059200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr2:100052800-100059000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:100052800-100059000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr2:100052800-100059200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr2:100053000-100059600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr2:100053200-100059000	Strong transcription	Fetal Intestine Large	intestine
30	chr2:100053400-100059800	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr2:100053600-100059200	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr2:100053600-100059400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr2:100053600-100059600	Strong transcription	HepG2	liver
34	chr2:100053800-100059200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr2:100053800-100059200	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr2:100053800-100075800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr2:100054400-100059000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr2:100054400-100059600	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr2:100054600-100059000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr2:100054600-100059000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr2:100054600-100059200	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr2:100054600-100059200	Strong transcription	HSMM	muscle
43	chr2:100054600-100059600	Strong transcription	K562	blood
44	chr2:100054800-100059000	Strong transcription	Primary B cells from peripheral blood	blood
45	chr2:100054800-100059200	Strong transcription	GM12878-XiMat	blood
46	chr2:100054800-100059400	Strong transcription	Placenta	Placenta
47	chr2:100054800-100059800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr2:100055000-100059000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr2:100055000-100059000	Strong transcription	Fetal Thymus	thymus
50	chr2:100055200-100059600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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