Variant report

Variant	rs2295423
Chromosome Location	chr1:93581024-93581025
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	FOXA2	chr1:93581021-93581262	HepG2	liver:	n/a	chr1:93581213-93581225

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:93579998..93581880-chr1:93596682..93599849,3	K562	blood:
2	chr1:93561194..93562759-chr1:93579663..93581219,2	K562	blood:

Variant related genes	Relation type
MTF2	TF binding region

Extended variants
information (count: 102 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs1010476	0.82[CHB][hapmap];0.90[CHD][hapmap]
rs1057257	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1060622	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10782955	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10874759	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10874762	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10874764	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1088318	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11164870	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11164871	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11164876	0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11164879	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11164880	0.83[AMR][1000 genomes]
rs11164881	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12030549	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12030843	0.86[CHB][hapmap]
rs12038699	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];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12044557	0.86[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap]
rs12044657	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12118230	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12118262	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12124011	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12128131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12130734	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12139009	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12385720	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1335679	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1474927	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1572343	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1856027	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1932314	1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2152358	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2208044	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2255722	0.82[CHB][hapmap];0.87[CHD][hapmap]
rs2281524	0.82[CHB][hapmap];0.87[CHD][hapmap]
rs2281525	0.82[CHB][hapmap]
rs2295424	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296558	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2297707	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2484486	0.81[CHB][hapmap];0.85[CHD][hapmap]
rs2749732	0.87[CHD][hapmap]
rs2765545	0.91[CEU][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap];0.88[TSI][hapmap];0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2783489	0.95[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap]
rs2783490	0.82[CHB][hapmap];0.87[CHD][hapmap]
rs2783495	0.82[CHB][hapmap];0.87[CHD][hapmap]
rs2783499	0.86[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap]
rs2783500	0.85[CHB][hapmap]
rs2783501	0.86[CHB][hapmap]
rs2815429	0.88[CHD][hapmap]
rs35940311	0.90[AMR][1000 genomes]
rs3754184	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3754186	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs3904666	0.82[CHB][hapmap];0.87[CHD][hapmap]
rs4000699	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs4240966	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs4484937	0.86[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap]
rs4847235	0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4847398	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4847399	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4847401	0.81[EUR][1000 genomes]
rs4847402	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs531358	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs531514	0.87[AMR][1000 genomes]
rs535760	0.80[AMR][1000 genomes]
rs547866	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs555161	0.93[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs565919	0.88[AMR][1000 genomes]
rs602204	0.80[AMR][1000 genomes]
rs612037	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61799471	0.83[AMR][1000 genomes]
rs622608	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs624131	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs627779	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs637646	1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes]
rs6541401	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6541404	0.83[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap]
rs6682670	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6688230	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs687394	1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes]
rs693737	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes]
rs7512911	0.82[AMR][1000 genomes]
rs7513705	0.91[CEU][hapmap];0.95[CHB][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7517363	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7532195	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7532549	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7535628	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7539307	0.91[CEU][hapmap];0.95[CHB][hapmap];0.82[AMR][1000 genomes]
rs7541687	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7553465	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7553916	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs797661	0.93[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs797666	0.80[AMR][1000 genomes]
rs797668	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs797671	0.83[AMR][1000 genomes]
rs797672	0.87[AMR][1000 genomes]
rs797675	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs797676	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs797680	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs797681	0.82[AMR][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	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830614	chr1:93465978-93678700	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS 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	34 gene(s)	inside rSNPs	diseases
3	nsv830625	chr1:93566378-93735246	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:21)

SNP	Gene	Cis/trans	Tissue	Source
rs2295423	F3	cis	cerebellum	SCAN
rs2295423	RP4-717I23.3	cis	Artery Aorta	GTEx
rs2295423	BARHL2	cis	parietal	SCAN
rs2295423	CCDC18	cis	parietal	SCAN
rs2295423	RP4-717I23.3	cis	Nerve Tibial	GTEx
rs2295423	TMED5	cis	cerebellum	SCAN
rs2295423	DR1	cis	multi-tissue	Pritchard
rs2295423	RP4-717I23.3	cis	Whole Blood	GTEx
rs2295423	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx
rs2295423	DR1	Cis_1M	lymphoblastoid	RTeQTL
rs2295423	DR1	cis	parietal	SCAN
rs2295423	TMED5	Cis_1M	lymphoblastoid	RTeQTL
rs2295423	RP4-717I23.3	cis	Esophagus Mucosa	GTEx
rs2295423	RP4-717I23.3	cis	Thyroid	GTEx
rs2295423	RP4-717I23.3	cis	Esophagus Muscularis	GTEx
rs2295423	RP4-717I23.3	cis	Muscle Skeletal	GTEx
rs2295423	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2295423	RP4-717I23.3	cis	Artery Tibial	GTEx
rs2295423	GCLM	cis	cerebellum	SCAN
rs2295423	TMED5	cis	parietal	SCAN
rs2295423	RP4-717I23.3	cis	lung	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93546200-93602200	Weak transcription	Aorta	Aorta
2	chr1:93547400-93581800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:93547600-93600000	Weak transcription	HSMMtube	muscle
4	chr1:93548000-93601800	Weak transcription	NHLF	lung
5	chr1:93548800-93581600	Weak transcription	Small Intestine	intestine
6	chr1:93549000-93582400	Weak transcription	HMEC	breast
7	chr1:93549000-93582800	Weak transcription	NHEK	skin
8	chr1:93560200-93581600	Weak transcription	Brain Anterior Caudate	brain
9	chr1:93563400-93582000	Weak transcription	Esophagus	oesophagus
10	chr1:93564000-93581800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr1:93565200-93625200	Weak transcription	Stomach Mucosa	stomach
12	chr1:93568400-93584200	Weak transcription	Fetal Brain Male	brain
13	chr1:93570000-93582200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr1:93570200-93581600	Weak transcription	Ovary	ovary
15	chr1:93571400-93602200	Weak transcription	Colonic Mucosa	Colon
16	chr1:93571600-93581600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr1:93572400-93599600	Weak transcription	Spleen	Spleen
18	chr1:93573400-93627000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr1:93573600-93586000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:93573800-93582000	Weak transcription	Brain Germinal Matrix	brain
21	chr1:93573800-93609000	Strong transcription	Fetal Thymus	thymus
22	chr1:93574200-93581200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr1:93574200-93581600	Weak transcription	Fetal Brain Female	brain
24	chr1:93574200-93582600	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr1:93574200-93609000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:93574600-93584800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:93574600-93585800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr1:93574600-93609000	Strong transcription	Dnd41	blood
29	chr1:93574600-93630200	Weak transcription	Right Ventricle	heart
30	chr1:93575200-93589800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr1:93575800-93589200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr1:93576000-93581600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr1:93576200-93581600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr1:93576400-93582000	Weak transcription	Hela-S3	cervix
35	chr1:93577200-93592800	Weak transcription	Colon Smooth Muscle	Colon
36	chr1:93577200-93597000	Weak transcription	Rectal Smooth Muscle	rectum
37	chr1:93577400-93582000	Weak transcription	Brain Hippocampus Middle	brain
38	chr1:93577400-93582200	Weak transcription	Brain Substantia Nigra	brain
39	chr1:93577600-93585200	Strong transcription	Primary hematopoietic stem cells	blood
40	chr1:93577600-93586600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr1:93577600-93586800	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr1:93577600-93588800	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr1:93577600-93591400	Weak transcription	Fetal Heart	heart
44	chr1:93577800-93601600	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr1:93578200-93587200	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr1:93578200-93588200	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr1:93578400-93583600	Strong transcription	GM12878-XiMat	blood
48	chr1:93578400-93583800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr1:93578400-93587400	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr1:93578400-93587600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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