Variant report

Variant	rs1555596
Chromosome Location	chr13:94981553-94981554
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2181621	0.82[EUR][1000 genomes]
rs9561538	0.83[ASN][1000 genomes]
rs9561539	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9634637	0.92[CHD][hapmap];0.89[GIH][hapmap];0.87[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948455	chr13:94451368-94988900	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv916640	chr13:94521959-95101443	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv533063	chr13:94560362-95101443	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv34004	chr13:94906537-95392644	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1555596	GPC6	cis	parietal	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:94958800-94981600	Weak transcription	Spleen	Spleen
2	chr13:94969800-94981600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr13:94973000-94982200	Weak transcription	Pancreas	Pancrea
4	chr13:94974600-94982000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr13:94975000-94981800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr13:94976000-94983200	Enhancers	HSMMtube	muscle
7	chr13:94976200-94983200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr13:94976600-94984000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
9	chr13:94977000-94981600	Enhancers	Ovary	ovary
10	chr13:94978200-94982600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr13:94979200-94982000	Enhancers	Fetal Lung	lung
12	chr13:94979200-94989600	Enhancers	Fetal Muscle Leg	muscle
13	chr13:94979400-94981600	Enhancers	HSMM	muscle
14	chr13:94979400-94983000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr13:94979400-94988600	Enhancers	Fetal Stomach	stomach
16	chr13:94979800-94982600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr13:94979800-94996800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr13:94980000-94981600	Weak transcription	Colon Smooth Muscle	Colon
19	chr13:94980000-94984000	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr13:94980200-94982600	Weak transcription	Fetal Heart	heart
21	chr13:94980200-94983800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr13:94980200-94984000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr13:94980400-94981600	Enhancers	Primary B cells from peripheral blood	blood
24	chr13:94980400-94981600	Weak transcription	Placenta	Placenta
25	chr13:94980400-94981800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr13:94980400-94982000	Enhancers	Dnd41	blood
27	chr13:94980400-94982200	Weak transcription	HUVEC	blood vessel
28	chr13:94980400-94982400	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr13:94980400-94982600	Enhancers	Primary T cells from cord blood	blood
30	chr13:94980400-94982800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr13:94980400-94983200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
32	chr13:94980400-94983600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr13:94980400-94983800	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr13:94980400-94983800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr13:94980400-94983800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr13:94980400-94984000	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr13:94980400-95000600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr13:94980600-94981800	Enhancers	Fetal Muscle Trunk	muscle
39	chr13:94980600-94982800	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr13:94980800-94981600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr13:94980800-94981600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr13:94980800-94981800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr13:94980800-94981800	Enhancers	GM12878-XiMat	blood
44	chr13:94980800-94982000	Weak transcription	Brain Substantia Nigra	brain
45	chr13:94980800-94982200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr13:94980800-94982200	Weak transcription	Duodenum Mucosa	Duodenum
47	chr13:94980800-94983000	Enhancers	NHLF	lung
48	chr13:94980800-94983600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr13:94981000-94981600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr13:94981000-94981600	Enhancers	Muscle Satellite Cultured Cells	--

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