Variant report

Variant	rs1966839
Chromosome Location	chr7:50627101-50627102
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	chr7:50625823..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: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10229102	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10229369	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10247443	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10249420	1.00[JPT][hapmap];0.90[YRI][hapmap]
rs10250513	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10265930	1.00[JPT][hapmap]
rs10274172	0.81[EUR][1000 genomes]
rs10278338	0.83[CEU][hapmap];0.89[EUR][1000 genomes]
rs10499695	0.91[CHB][hapmap]
rs11238214	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs11238226	0.81[EUR][1000 genomes]
rs11489734	0.82[EUR][1000 genomes]
rs11489736	0.81[EUR][1000 genomes]
rs11974297	0.91[CHB][hapmap];0.81[EUR][1000 genomes]
rs12665904	0.82[EUR][1000 genomes]
rs1451373	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1451374	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1451375	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1470747	1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes]
rs17133878	0.91[CHB][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1813214	0.81[EUR][1000 genomes]
rs1839740	0.81[EUR][1000 genomes]
rs1987859	0.81[EUR][1000 genomes]
rs2329340	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2329341	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2329342	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3779074	0.81[JPT][hapmap]
rs3829897	0.84[EUR][1000 genomes]
rs4275187	0.81[EUR][1000 genomes]
rs4452748	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4469404	0.81[EUR][1000 genomes]
rs4512339	0.81[EUR][1000 genomes]
rs4601266	0.81[EUR][1000 genomes]
rs4947644	0.91[CHB][hapmap]
rs55738142	0.84[EUR][1000 genomes]
rs56233242	0.82[EUR][1000 genomes]
rs59086818	0.81[EUR][1000 genomes]
rs6593010	0.84[CEU][hapmap];0.89[EUR][1000 genomes]
rs6949897	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6962356	0.95[CEU][hapmap];0.91[CHB][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6969081	0.83[CEU][hapmap];0.91[CHB][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73125288	0.84[EUR][1000 genomes]
rs73125290	0.84[EUR][1000 genomes]
rs7786398	0.81[CHB][hapmap];0.87[ASN][1000 genomes]
rs7797131	0.81[EUR][1000 genomes]
rs7802148	0.81[EUR][1000 genomes]
rs7803440	1.00[JPT][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes]
rs7803788	1.00[JPT][hapmap];0.90[YRI][hapmap]
rs7803903	0.82[AFR][1000 genomes]
rs896309	0.82[JPT][hapmap]
rs921450	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs921451	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1966839	FIGNL1	cis	lung	GTEx

Chromatin state (count:25 , 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	chr7:50624600-50631800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr7:50625000-50628600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr7:50625000-50628600	Weak transcription	Small Intestine	intestine
9	chr7:50625200-50628400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr7:50625400-50628400	Enhancers	Duodenum Mucosa	Duodenum
11	chr7:50625600-50628400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr7:50625600-50628600	Weak transcription	Brain Germinal Matrix	brain
13	chr7:50625800-50627600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr7:50626000-50628000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr7:50626400-50628200	Genic enhancers	Fetal Intestine Small	intestine
16	chr7:50626600-50627800	Weak transcription	Liver	Liver
17	chr7:50626600-50628200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr7:50626600-50628400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr7:50626600-50629600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr7:50626800-50627800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr7:50626800-50627800	Weak transcription	Ovary	ovary
22	chr7:50626800-50631800	Weak transcription	Gastric	stomach
23	chr7:50626800-50632000	Weak transcription	Stomach Mucosa	stomach
24	chr7:50627000-50628200	Weak transcription	Pancreas	Pancrea
25	chr7:50627000-50628800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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