Variant report

Variant	rs10248903
Chromosome Location	chr7:50461684-50461685
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	chr7:50454599..50456922-chr7:50460063..50461739,2	K562	blood:
2	chr7:50454599..50457832-chr7:50460063..50462118,3	K562	blood:

Extended variants
information (count: 7 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10230385	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10254237	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2060762	0.89[TSI][hapmap]
rs3735275	0.89[TSI][hapmap]
rs6954833	1.00[EUR][1000 genomes]
rs6956528	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs10248903	FIGNL1	cis	parietal	SCAN
rs10248903	FIGNL1	cis	Thyroid	GTEx
rs10248903	IKZF1	Cis_1M	lymphoblastoid	RTeQTL
rs10248903	FIGNL1	cis	Skin Sun Exposed Lower leg	GTEx
rs10248903	FIGNL1	cis	Adipose Subcutaneous	GTEx
rs10248903	FIGNL1	cis	lung	GTEx
rs10248903	FIGNL1	cis	Nerve Tibial	GTEx
rs10248903	FIGNL1	cis	Artery Tibial	GTEx
rs10248903	FIGNL1	cis	cerebellum	SCAN

Chromatin state (count:43 , 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	chr7:50431400-50472600	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr7:50447200-50467400	Weak transcription	Esophagus	oesophagus
4	chr7:50447200-50467400	Weak transcription	Gastric	stomach
5	chr7:50449200-50467400	Weak transcription	Liver	Liver
6	chr7:50451400-50462600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr7:50453200-50467800	Weak transcription	Pancreas	Pancrea
8	chr7:50454600-50462400	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr7:50455400-50463400	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr7:50456600-50462200	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr7:50459000-50462600	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
12	chr7:50459200-50462400	Genic enhancers	Fetal Thymus	thymus
13	chr7:50459400-50462400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr7:50459800-50462400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr7:50459800-50462600	Genic enhancers	Primary monocytes fromperipheralblood	blood
16	chr7:50460000-50462000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr7:50460000-50462000	Genic enhancers	K562	blood
18	chr7:50460000-50462200	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
19	chr7:50460000-50462600	Genic enhancers	GM12878-XiMat	blood
20	chr7:50460200-50462200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr7:50460200-50462600	Genic enhancers	Thymus	Thymus
22	chr7:50460200-50464200	Genic enhancers	Monocytes-CD14+_RO01746	blood
23	chr7:50460400-50462000	Genic enhancers	Primary hematopoietic stem cells	blood
24	chr7:50460400-50462400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr7:50460400-50466200	Weak transcription	Lung	lung
26	chr7:50460600-50462400	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
27	chr7:50460800-50461800	Genic enhancers	Sigmoid Colon	Sigmoid Colon
28	chr7:50460800-50462400	Genic enhancers	Spleen	Spleen
29	chr7:50460800-50462600	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
30	chr7:50461000-50461800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
31	chr7:50461000-50462000	Transcr. at gene 5' and 3'	Primary T helper cells fromperipheralblood	blood
32	chr7:50461000-50462400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
33	chr7:50461200-50461800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr7:50461200-50462200	Transcr. at gene 5' and 3'	Primary B cells from peripheral blood	blood
35	chr7:50461200-50462200	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
36	chr7:50461400-50461800	Enhancers	Duodenum Mucosa	Duodenum
37	chr7:50461400-50462600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr7:50461600-50462000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr7:50461600-50462000	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr7:50461600-50462000	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr7:50461600-50462400	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr7:50461600-50468600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr7:50461600-50472600	Strong transcription	Dnd41	blood

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