Variant report

Variant	rs2346320
Chromosome Location	chr4:159087642-159087643
allele	A/G
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	GATA2	chr4:159087323-159087644	SH-SY5Y	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000248429	TF binding region

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10005007	1.00[ASN][1000 genomes]
rs10007737	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10008208	1.00[JPT][hapmap]
rs10012339	1.00[JPT][hapmap]
rs10016822	0.84[EUR][1000 genomes]
rs10018872	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10024133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10026876	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10028490	1.00[JPT][hapmap]
rs10517689	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11100150	0.90[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11100151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11937022	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11938464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12502811	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[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];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12511679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12645131	1.00[JPT][hapmap]
rs12648410	1.00[JPT][hapmap]
rs13113959	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs1320370	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1320371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs14202	1.00[JPT][hapmap]
rs17036927	1.00[CEU][hapmap]
rs2346319	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2346321	1.00[JPT][hapmap]
rs2346381	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2346774	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2346776	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2346780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2346783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2346784	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28499342	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28691778	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28719822	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2881373	1.00[JPT][hapmap]
rs2881473	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4234917	1.00[JPT][hapmap]
rs4317248	1.00[JPT][hapmap]
rs4324593	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4345228	1.00[JPT][hapmap]
rs4391084	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4472184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4501266	1.00[JPT][hapmap]
rs4582199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4627913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4690893	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4691455	1.00[JPT][hapmap]
rs4691456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4691457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4691458	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4691459	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4691461	1.00[JPT][hapmap]
rs4691462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4691463	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4691464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4691465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4691467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6536299	1.00[JPT][hapmap]
rs6812635	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6813306	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6819576	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6820988	1.00[JPT][hapmap]
rs6821598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6830702	1.00[JPT][hapmap]
rs6832099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6833198	1.00[JPT][hapmap]
rs6834164	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6849902	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6852646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6855420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7671094	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7671501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7671934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7686997	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7695599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8180159	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8370	1.00[JPT][hapmap]

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	nsv993476	chr4:158550643-159202015	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1030124	chr4:158758675-159251140	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv1021067	chr4:158972282-159175475	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:159076800-159089800	Weak transcription	Fetal Muscle Trunk	muscle
2	chr4:159078400-159089000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr4:159078600-159094000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr4:159083000-159091800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr4:159083200-159089800	Weak transcription	Fetal Kidney	kidney
6	chr4:159083400-159089000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr4:159083400-159090400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr4:159084000-159089800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr4:159084200-159088600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr4:159084200-159089200	Weak transcription	Osteobl	bone
11	chr4:159084200-159089800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr4:159084200-159090000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr4:159084200-159090800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr4:159085000-159088600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr4:159085000-159095200	Active TSS	Aorta	Aorta
16	chr4:159085200-159089400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr4:159085200-159094000	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr4:159085400-159090800	Active TSS	Stomach Smooth Muscle	stomach
19	chr4:159085400-159095000	Active TSS	Right Atrium	heart
20	chr4:159085600-159088400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr4:159085600-159095000	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr4:159085800-159087800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr4:159085800-159087800	Flanking Active TSS	Fetal Heart	heart
24	chr4:159086000-159087800	Flanking Active TSS	HUVEC	blood vessel
25	chr4:159086000-159088200	Enhancers	Fetal Intestine Large	intestine
26	chr4:159086000-159089600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr4:159086000-159089800	Active TSS	Fetal Muscle Leg	muscle
28	chr4:159086000-159089800	Weak transcription	Pancreas	Pancrea
29	chr4:159086000-159090800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr4:159086200-159087800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr4:159086200-159088400	Weak transcription	Left Ventricle	heart
32	chr4:159086200-159090600	Weak transcription	NH-A	brain
33	chr4:159086200-159091400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr4:159086400-159088400	Weak transcription	Psoas Muscle	Psoas
35	chr4:159086400-159088400	Enhancers	Rectal Smooth Muscle	rectum
36	chr4:159086400-159089000	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr4:159086400-159089000	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr4:159086400-159089200	Weak transcription	NHDF-Ad	bronchial
39	chr4:159086400-159090000	Weak transcription	Lung	lung
40	chr4:159086400-159093200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:159086800-159087800	Flanking Active TSS	HepG2	liver
42	chr4:159086800-159089000	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr4:159087000-159087800	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr4:159087000-159087800	Enhancers	Brain Anterior Caudate	brain
45	chr4:159087000-159087800	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr4:159087000-159087800	Flanking Active TSS	HMEC	breast
47	chr4:159087000-159088000	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr4:159087000-159089800	Active TSS	HSMMtube	muscle
49	chr4:159087200-159087800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr4:159087200-159089400	Enhancers	Fetal Intestine Small	intestine

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