Variant report

Variant	rs7803788
Chromosome Location	chr7:50625898-50625899
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:50625823..50628004-chr7:50631003..50633702,2	K562	blood:
2	chr7:50625436..50627457-chr7:50643503..50646245,2	K562	blood:

Variant related genes	Relation type
ENSG00000132437	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10239830	0.91[ASN][1000 genomes]
rs10249420	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10250513	0.91[JPT][hapmap];0.91[YRI][hapmap]
rs10265930	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10267323	0.87[ASN][1000 genomes]
rs10271341	0.95[CHB][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.87[ASN][1000 genomes]
rs10276473	0.95[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10277662	0.87[ASN][1000 genomes]
rs11575320	0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.91[ASN][1000 genomes]
rs12666409	0.95[CEU][hapmap];0.94[GIH][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs12671474	0.87[ASN][1000 genomes]
rs12673638	0.80[EUR][1000 genomes]
rs1451373	0.95[JPT][hapmap];0.90[YRI][hapmap]
rs1451374	0.95[JPT][hapmap]
rs1451375	0.95[JPT][hapmap];0.95[MKK][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes]
rs1470747	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1966839	1.00[JPT][hapmap];0.90[YRI][hapmap]
rs2044859	0.90[CHB][hapmap];0.88[CHD][hapmap];0.88[ASN][1000 genomes]
rs2329340	0.95[JPT][hapmap];0.93[MKK][hapmap]
rs2329342	0.95[JPT][hapmap];0.95[MKK][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes]
rs2329371	0.95[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28415418	0.83[EUR][1000 genomes]
rs2876829	0.89[MEX][hapmap]
rs3735273	0.95[CHB][hapmap];0.86[CHD][hapmap];0.88[ASN][1000 genomes]
rs3735275	0.80[CHB][hapmap]
rs3779074	0.90[CHB][hapmap];0.88[ASN][1000 genomes]
rs3779078	0.95[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3807552	0.95[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.91[ASN][1000 genomes]
rs3807555	0.95[CHB][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3807556	0.95[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.91[ASN][1000 genomes]
rs3807558	0.88[GIH][hapmap]
rs4452748	0.95[JPT][hapmap];0.95[MKK][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes]
rs56105337	0.80[EUR][1000 genomes]
rs66792686	0.86[EUR][1000 genomes]
rs68011952	0.87[EUR][1000 genomes]
rs6949897	0.91[JPT][hapmap];0.91[YRI][hapmap]
rs6950777	0.95[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.88[ASN][1000 genomes]
rs745043	0.89[MEX][hapmap]
rs7779110	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7803440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7803903	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7807335	0.95[CEU][hapmap];0.94[GIH][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes]
rs896307	0.81[CEU][hapmap]
rs896309	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs921450	0.95[JPT][hapmap];0.95[MKK][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes]
rs921451	0.95[JPT][hapmap];0.95[MKK][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes]
rs978784	0.82[CEU][hapmap];0.88[GIH][hapmap];0.83[TSI][hapmap]
rs9942686	0.94[CHB][hapmap];0.88[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	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
2	nsv1015758	chr7:50565404-50768153	Flanking Active TSS Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv1023228	chr7:50573214-50777634	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv1032882	chr7:50611138-50775257	Genic enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv538834	chr7:50611138-50775257	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7803788	FIGNL1	cis	multi-tissue	Pritchard
rs7803788	FIGNL1	cis	lung	GTEx
rs7803788	FIGNL1	cis	cerebellum	SCAN
rs7803788	FIGNL1	cis	parietal	SCAN
rs7803788	FIGNL1	cis	Nerve Tibial	GTEx
rs7803788	FIGNL1	cis	Thyroid	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50601600-50631400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr7:50611000-50631800	Weak transcription	Colonic Mucosa	Colon
3	chr7:50619400-50628200	Enhancers	HepG2	liver
4	chr7:50619600-50627800	Enhancers	Fetal Intestine Large	intestine
5	chr7:50620800-50635600	Weak transcription	Lung	lung
6	chr7:50621800-50627000	Enhancers	Pancreas	Pancrea
7	chr7:50623000-50626400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr7:50623800-50626800	Enhancers	Ovary	ovary
9	chr7:50624400-50626000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr7:50624400-50626400	Enhancers	Fetal Intestine Small	intestine
11	chr7:50624600-50626000	Weak transcription	Stomach Mucosa	stomach
12	chr7:50624600-50631800	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr7:50624800-50626200	Weak transcription	Liver	Liver
14	chr7:50625000-50626000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr7:50625000-50626600	Enhancers	Pancreatic Islets	Pancreatic Islet
16	chr7:50625000-50628600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr7:50625000-50628600	Weak transcription	Small Intestine	intestine
18	chr7:50625200-50628400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr7:50625400-50626000	Weak transcription	Fetal Stomach	stomach
20	chr7:50625400-50626200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr7:50625400-50628400	Enhancers	Duodenum Mucosa	Duodenum
22	chr7:50625600-50626400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr7:50625600-50628400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr7:50625600-50628600	Weak transcription	Brain Germinal Matrix	brain
25	chr7:50625800-50626800	Enhancers	K562	blood
26	chr7:50625800-50627600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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