Variant report

Variant	rs6854347
Chromosome Location	chr4:79849042-79849043
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr4:79849014-79849302	SH-SY5Y	brain:	n/a	chr4:79849224-79849231 chr4:79849223-79849233 chr4:79849224-79849233 chr4:79849220-79849236 chr4:79849222-79849235

Variant related genes	Relation type
PAQR3	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10018189	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10023100	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10025599	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10028067	0.94[CEU][hapmap]
rs10034295	0.86[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs10857059	0.94[CEU][hapmap];0.90[MEX][hapmap]
rs11722437	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1275045	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1275046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1275047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1299129	0.94[CEU][hapmap];0.90[MEX][hapmap]
rs13108247	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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1480718	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1871706	0.94[CEU][hapmap];0.90[MEX][hapmap]
rs1979444	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2046104	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2288254	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs2554395	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3822106	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3937772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4512020	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62308043	0.90[ASN][1000 genomes]
rs6534083	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6534085	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6534086	1.00[ASN][1000 genomes]
rs6534087	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6534090	0.80[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6846743	0.85[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs7656083	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7664339	0.90[MEX][hapmap]
rs7664587	0.94[CEU][hapmap];0.90[MEX][hapmap]
rs7677084	0.84[MEX][hapmap]
rs7688534	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9307446	0.94[CEU][hapmap]
rs931149	0.82[ASN][1000 genomes]
rs931150	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9993426	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879504	chr4:79759796-79874275	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv829979	chr4:79819168-80019159	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv1000907	chr4:79838948-80224764	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6854347	LIN54	cis	cerebellum	SCAN
rs6854347	NAAA	cis	parietal	SCAN
rs6854347	ANXA3	cis	multi-tissue	Pritchard

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79779800-79858200	Weak transcription	Fetal Brain Male	brain
2	chr4:79794200-79850000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:79794200-79859600	Weak transcription	Colonic Mucosa	Colon
4	chr4:79794400-79850000	Weak transcription	Pancreas	Pancrea
5	chr4:79794800-79850200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr4:79794800-79858000	Weak transcription	HepG2	liver
7	chr4:79799200-79858000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr4:79814600-79859600	Weak transcription	Fetal Kidney	kidney
9	chr4:79816200-79858400	Weak transcription	Stomach Smooth Muscle	stomach
10	chr4:79827400-79858000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr4:79827400-79858000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr4:79829000-79859200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr4:79830200-79850000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr4:79830200-79859200	Weak transcription	Hela-S3	cervix
15	chr4:79831000-79850000	Weak transcription	Gastric	stomach
16	chr4:79831200-79858000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr4:79831400-79856600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr4:79833000-79849800	Weak transcription	Fetal Stomach	stomach
19	chr4:79833000-79850000	Weak transcription	Lung	lung
20	chr4:79833000-79850000	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr4:79833000-79850000	Weak transcription	Spleen	Spleen
22	chr4:79833000-79850000	Weak transcription	HSMMtube	muscle
23	chr4:79833000-79859800	Weak transcription	Esophagus	oesophagus
24	chr4:79833000-79859800	Weak transcription	Right Ventricle	heart
25	chr4:79833200-79849800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr4:79833200-79849800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr4:79833200-79849800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr4:79833200-79849800	Weak transcription	Ovary	ovary
29	chr4:79833200-79850000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr4:79833200-79853400	Weak transcription	NHLF	lung
31	chr4:79833200-79859000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr4:79833200-79859600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr4:79833400-79856800	Weak transcription	GM12878-XiMat	blood
34	chr4:79833600-79849800	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr4:79833600-79858000	Weak transcription	Brain Substantia Nigra	brain
36	chr4:79833600-79859000	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr4:79833600-79859800	Weak transcription	Placenta	Placenta
38	chr4:79835600-79850000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr4:79835600-79856000	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr4:79836600-79859000	Weak transcription	HSMM	muscle
41	chr4:79839000-79849600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr4:79839000-79850000	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr4:79839000-79850000	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr4:79839000-79850200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr4:79839000-79850400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr4:79840200-79856800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr4:79841200-79849200	Strong transcription	Dnd41	blood
48	chr4:79841200-79851800	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr4:79841600-79852200	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr4:79841800-79857600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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