Variant report

Variant	rs3735275
Chromosome Location	chr7:50517271-50517272
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10230343	0.95[JPT][hapmap]
rs10235796	0.82[EUR][1000 genomes]
rs10249420	0.80[CHB][hapmap]
rs10271341	0.85[CHB][hapmap]
rs10276473	0.85[CHB][hapmap]
rs11238133	0.83[YRI][hapmap]
rs11238134	0.91[YRI][hapmap]
rs11575320	0.85[CHB][hapmap]
rs11575463	0.90[YRI][hapmap]
rs11761683	0.91[YRI][hapmap]
rs11772714	0.91[YRI][hapmap]
rs12538151	0.86[EUR][1000 genomes]
rs1466164	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1807066	0.81[ASN][1000 genomes]
rs2044859	0.80[CHB][hapmap]
rs2060761	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2060762	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2305358	0.86[JPT][hapmap]
rs2329371	0.85[CHB][hapmap]
rs2876829	0.87[YRI][hapmap]
rs3735273	0.90[CHB][hapmap]
rs3779078	0.85[CHB][hapmap]
rs3807552	0.85[CHB][hapmap]
rs3807555	0.85[CHB][hapmap]
rs3807556	0.85[CHB][hapmap]
rs3807558	0.87[YRI][hapmap]
rs4515495	0.99[ASN][1000 genomes]
rs4618649	0.88[EUR][1000 genomes]
rs4947410	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4947437	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4947510	0.95[JPT][hapmap]
rs6593336	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6945253	0.82[JPT][hapmap]
rs6950777	0.85[CHB][hapmap]
rs6965721	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7384694	0.81[EUR][1000 genomes]
rs745042	0.83[YRI][hapmap]
rs745043	0.85[ASW][hapmap];0.84[CHD][hapmap];0.87[YRI][hapmap]
rs7790230	0.95[JPT][hapmap]
rs7790758	0.95[YRI][hapmap]
rs7803788	0.80[CHB][hapmap]
rs896307	0.86[YRI][hapmap]
rs896309	0.84[CHB][hapmap];0.85[JPT][hapmap];0.91[YRI][hapmap]
rs963739	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9942686	0.82[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016665	chr7:50452552-51404524	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs3735275	FIGNL1	cis	Skin Sun Exposed Lower leg	GTEx
rs3735275	FIGNL1	cis	Artery Tibial	GTEx
rs3735275	FIGNL1	cis	parietal	SCAN
rs3735275	FIGNL1	cis	lung	GTEx
rs3735275	FIGNL1	cis	lymphoblastoid	seeQTL
rs3735275	FIGNL1	cis	cerebellum	SCAN
rs3735275	FIGNL1	cis	Adipose Subcutaneous	GTEx
rs3735275	FIGNL1	cis	Thyroid	GTEx
rs3735275	FIGNL1	cis	multi-tissue	Pritchard
rs3735275	FIGNL1	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50496200-50517600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:50501000-50517400	Weak transcription	Esophagus	oesophagus
3	chr7:50504800-50517400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr7:50509400-50517400	Weak transcription	Aorta	Aorta
5	chr7:50513600-50517400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr7:50514800-50517400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr7:50515000-50517400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr7:50515000-50517600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr7:50515000-50517600	Weak transcription	Lung	lung
10	chr7:50515800-50517400	Flanking Active TSS	GM12878-XiMat	blood
11	chr7:50516400-50517600	Flanking Active TSS	Dnd41	blood
12	chr7:50516800-50517400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr7:50516800-50517400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr7:50516800-50517400	Enhancers	Primary B cells from cord blood	blood
15	chr7:50516800-50517400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr7:50516800-50517400	Flanking Active TSS	Brain Germinal Matrix	brain
17	chr7:50516800-50517400	Flanking Active TSS	A549	lung
18	chr7:50516800-50517400	Flanking Active TSS	HepG2	liver
19	chr7:50516800-50517400	Flanking Active TSS	HUVEC	blood vessel
20	chr7:50516800-50517600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr7:50516800-50517600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr7:50516800-50517600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr7:50516800-50517800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr7:50516800-50517800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr7:50516800-50517800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr7:50516800-50518800	Active TSS	NHLF	lung
27	chr7:50516800-50519000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr7:50517000-50517400	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr7:50517000-50517400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
30	chr7:50517000-50517400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr7:50517000-50517400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr7:50517000-50517400	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr7:50517000-50517400	Enhancers	Primary B cells from peripheral blood	blood
34	chr7:50517000-50517400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr7:50517000-50517400	Enhancers	Adipose Nuclei	Adipose
36	chr7:50517000-50517400	Enhancers	Colon Smooth Muscle	Colon
37	chr7:50517000-50517400	Flanking Active TSS	Fetal Kidney	kidney
38	chr7:50517000-50517400	Flanking Active TSS	Fetal Lung	lung
39	chr7:50517000-50517400	Flanking Active TSS	K562	blood
40	chr7:50517000-50517400	Enhancers	Monocytes-CD14+_RO01746	blood
41	chr7:50517000-50517400	Flanking Active TSS	NHDF-Ad	bronchial
42	chr7:50517000-50517600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr7:50517000-50517600	Flanking Active TSS	Primary T cells from cord blood	blood
44	chr7:50517000-50517600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
45	chr7:50517000-50517600	Flanking Active TSS	Fetal Brain Female	brain
46	chr7:50517000-50517600	Flanking Active TSS	NHEK	skin
47	chr7:50517000-50518600	Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr7:50517000-50518800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr7:50517000-50518800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr7:50517000-50518800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin

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