Variant report

Variant	rs12669770
Chromosome Location	chr7:50656334-50656335
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	chr7:50651220..50655570-chr7:50655911..50660457,6	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10238413	0.81[ASN][1000 genomes]
rs10274172	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10278338	0.88[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];0.80[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11238214	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11238226	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11489734	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11489736	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11977415	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12665904	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12666409	0.85[JPT][hapmap]
rs1451375	0.84[GIH][hapmap];0.85[TSI][hapmap]
rs1813214	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1839740	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1966839	0.83[CEU][hapmap]
rs1987859	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2329340	0.84[GIH][hapmap];0.85[TSI][hapmap]
rs2329342	0.84[GIH][hapmap];0.85[TSI][hapmap]
rs3829897	0.84[CEU][hapmap];0.85[CHB][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs4275187	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4392851	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4452748	0.84[GIH][hapmap];0.85[TSI][hapmap]
rs4469404	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4512339	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4601266	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4947684	0.81[ASN][1000 genomes]
rs55718635	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55738142	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56233242	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59086818	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6593010	0.88[CEU][hapmap];0.91[CHB][hapmap];0.80[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs68143668	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6969081	0.80[CEU][hapmap]
rs73125288	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73125290	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7797131	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7802148	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7804365	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs7807335	0.85[JPT][hapmap]
rs921450	0.84[GIH][hapmap];0.85[TSI][hapmap]
rs921451	0.84[GIH][hapmap];0.85[TSI][hapmap]
rs978784	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv1031138	chr7:50651793-50814881	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12669770	FIGNL1	cis	parietal	SCAN
rs12669770	FIGNL1	cis	lung	GTEx
rs12669770	FIGNL1	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50650800-50659600	Weak transcription	Ovary	ovary
2	chr7:50652000-50671800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr7:50652200-50657800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr7:50652400-50687400	Weak transcription	Right Atrium	heart
5	chr7:50652600-50658600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr7:50652800-50658400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr7:50652800-50660400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr7:50653000-50658800	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr7:50653000-50659800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr7:50653000-50660000	Weak transcription	Brain Cingulate Gyrus	brain
11	chr7:50653200-50672400	Weak transcription	NHEK	skin
12	chr7:50653400-50656800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr7:50653400-50659800	Weak transcription	Fetal Lung	lung
14	chr7:50653400-50670600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr7:50653600-50656800	Weak transcription	Placenta	Placenta
16	chr7:50654000-50680000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr7:50654400-50660200	Weak transcription	Gastric	stomach
18	chr7:50654800-50659000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr7:50654800-50659200	Weak transcription	Hela-S3	cervix
20	chr7:50655000-50656400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr7:50655200-50659000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr7:50655200-50660400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr7:50655800-50657000	Enhancers	Pancreas	Pancrea
24	chr7:50655800-50659600	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr7:50655800-50659800	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr7:50656000-50658000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr7:50656000-50658600	Weak transcription	Liver	Liver
28	chr7:50656000-50658600	Weak transcription	Fetal Intestine Small	intestine
29	chr7:50656000-50658800	Weak transcription	Duodenum Mucosa	Duodenum
30	chr7:50656000-50659000	Weak transcription	Stomach Smooth Muscle	stomach
31	chr7:50656200-50658200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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