Variant report

Variant	rs2244353
Chromosome Location	chr7:50739455-50739456
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	chr7:50738644..50740280-chr7:50859726..50861822,2	K562	blood:
2	chr7:50732851..50735812-chr7:50737426..50740683,4	K562	blood:

Variant related genes	Relation type
ENSG00000106070	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs13241205	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13243873	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1800504	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2214964	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2237475	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2237476	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2237480	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2237484	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2237487	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2237489	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2240499	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2244347	0.82[CHD][hapmap];0.81[JPT][hapmap];0.81[LWK][hapmap];0.81[TSI][hapmap]
rs2244351	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2244372	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2244480	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2282931	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2529408	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2529410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2529412	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2529418	0.82[AMR][1000 genomes]
rs2715131	0.87[AFR][1000 genomes]
rs2715132	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs730652	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2244353	FIGNL1	cis	brain	seeQTL
rs2244353	ABCA13	cis	cerebellum	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50706400-50744000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr7:50707200-50748600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr7:50710000-50743600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr7:50710000-50758200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr7:50715600-50740600	Weak transcription	Brain Germinal Matrix	brain
6	chr7:50716600-50740200	Weak transcription	Fetal Intestine Large	intestine
7	chr7:50724200-50742800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr7:50726000-50741000	Weak transcription	Fetal Brain Female	brain
9	chr7:50729800-50741600	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr7:50730200-50744000	Weak transcription	Small Intestine	intestine
11	chr7:50730200-50748600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr7:50731000-50741400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr7:50731400-50743200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr7:50731800-50750000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr7:50732600-50749200	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr7:50733200-50743600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr7:50733600-50741800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr7:50733800-50742600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr7:50734200-50743400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr7:50734200-50748800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr7:50734400-50740600	Weak transcription	Esophagus	oesophagus
22	chr7:50734400-50740800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr7:50734400-50742400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr7:50734800-50739600	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr7:50734800-50740200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr7:50735400-50743000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr7:50735400-50744400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr7:50735600-50739600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr7:50735600-50742400	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr7:50735800-50741200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr7:50735800-50743200	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr7:50735800-50745000	Weak transcription	Stomach Mucosa	stomach
33	chr7:50736000-50742800	Strong transcription	Fetal Stomach	stomach
34	chr7:50736000-50743200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr7:50736000-50743400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr7:50736000-50743600	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr7:50736200-50739800	Weak transcription	Gastric	stomach
38	chr7:50736200-50740200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr7:50736200-50741400	Weak transcription	NHLF	lung
40	chr7:50736200-50742600	Weak transcription	Brain Cingulate Gyrus	brain
41	chr7:50736200-50743200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr7:50736400-50741200	Weak transcription	Placenta	Placenta
43	chr7:50736400-50742400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr7:50736600-50739600	Weak transcription	Fetal Intestine Small	intestine
45	chr7:50736600-50740400	Weak transcription	Primary T cells from cord blood	blood
46	chr7:50736600-50740400	Weak transcription	Fetal Muscle Leg	muscle
47	chr7:50736600-50740800	Weak transcription	Adipose Nuclei	Adipose
48	chr7:50736600-50742200	Weak transcription	Rectal Smooth Muscle	rectum
49	chr7:50736600-50742200	Strong transcription	HSMMtube	muscle
50	chr7:50736600-50755200	Weak transcription	NHDF-Ad	bronchial

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