Variant report

Variant	rs12718910
Chromosome Location	chr7:50454452-50454453
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11763774	0.97[EUR][1000 genomes]
rs11764792	0.88[EUR][1000 genomes]
rs11770117	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12154303	0.87[EUR][1000 genomes]
rs12533940	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12670555	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12719019	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12719030	0.89[EUR][1000 genomes]
rs4947641	0.89[EUR][1000 genomes]
rs6964823	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6969942	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6978646	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7789635	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][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	nsv464444	chr7:49671882-50454736	Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv606897	chr7:49671883-50454736	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1020869	chr7:49712860-50457544	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv522250	chr7:50442726-50454736	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	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
rs12718910	FIGNL1	cis	Nerve Tibial	GTEx
rs12718910	FIGNL1	cis	Skin Sun Exposed Lower leg	GTEx
rs12718910	FIGNL1	cis	Esophagus Muscularis	GTEx
rs12718910	FIGNL1	Cis_1M	lymphoblastoid	RTeQTL
rs12718910	FIGNL1	cis	Esophagus Mucosa	GTEx
rs12718910	FIGNL1	cis	Artery Aorta	GTEx
rs12718910	FIGNL1	cis	Thyroid	GTEx
rs12718910	FIGNL1	cis	Artery Tibial	GTEx
rs12718910	FIGNL1	cis	lung	GTEx
rs12718910	FIGNL1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50420000-50461800	Genic enhancers	Primary T cells fromperipheralblood	blood
2	chr7:50430600-50459800	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr7:50431200-50460600	Strong transcription	Dnd41	blood
4	chr7:50431400-50472600	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr7:50437200-50460200	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr7:50439400-50460600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
7	chr7:50440800-50461400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr7:50441200-50459800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr7:50441200-50460200	Strong transcription	Thymus	Thymus
10	chr7:50441200-50460400	Strong transcription	Primary hematopoietic stem cells	blood
11	chr7:50441200-50460400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr7:50441800-50459200	Strong transcription	Fetal Thymus	thymus
13	chr7:50442200-50460200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr7:50445400-50461400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr7:50446600-50461400	Weak transcription	Colonic Mucosa	Colon
16	chr7:50447200-50467400	Weak transcription	Esophagus	oesophagus
17	chr7:50447200-50467400	Weak transcription	Gastric	stomach
18	chr7:50448200-50455000	Weak transcription	Lung	lung
19	chr7:50449200-50467400	Weak transcription	Liver	Liver
20	chr7:50449800-50459200	Strong transcription	Primary B cells from cord blood	blood
21	chr7:50450400-50460000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr7:50450600-50455000	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr7:50450600-50455000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr7:50450800-50455200	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr7:50451000-50455000	Strong transcription	Primary B cells from peripheral blood	blood
26	chr7:50451400-50455000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr7:50451400-50462600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr7:50452000-50454600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr7:50452600-50458400	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr7:50452800-50454600	Weak transcription	Duodenum Mucosa	Duodenum
31	chr7:50452800-50455600	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr7:50453200-50454600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr7:50453200-50456000	Weak transcription	Spleen	Spleen
34	chr7:50453200-50459000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr7:50453200-50467800	Weak transcription	Pancreas	Pancrea
36	chr7:50453400-50454600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr7:50453400-50454600	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr7:50453600-50454600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr7:50453600-50454800	Strong transcription	Primary T cells from cord blood	blood
40	chr7:50453600-50456200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr7:50453600-50460000	Weak transcription	GM12878-XiMat	blood
42	chr7:50453800-50455000	Weak transcription	K562	blood
43	chr7:50453800-50455600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
44	chr7:50454000-50454600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr7:50454200-50454800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr7:50454400-50454600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr7:50454400-50456800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr7:50454400-50461000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood

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