Variant report

Variant	rs1443700
Chromosome Location	chr2:172846257-172846258
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:172842580..172845060-chr2:172845399..172847700,2	K562	blood:
2	chr2:172842580..172844275-chr2:172846200..172848485,2	K562	blood:
3	chr2:172844181..172846403-chr2:172947741..172950445,2	MCF-7	breast:
4	chr2:172844335..172847013-chr2:172956341..172958863,2	MCF-7	breast:
5	chr2:172844744..172846425-chr2:172851326..172853305,2	K562	blood:

Variant related genes	Relation type
ENSG00000144355	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10166352	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10177679	0.83[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10188587	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10196521	1.00[ASW][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs1022358	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs10439296	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[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];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10930496	0.84[AMR][1000 genomes]
rs10930498	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10930500	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10930501	0.84[ASN][1000 genomes]
rs11676484	0.88[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11677573	1.00[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11692418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11695887	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11883977	0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12467010	0.87[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs12468218	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12473516	0.94[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs12478215	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12479374	1.00[JPT][hapmap]
rs12617265	1.00[ASW][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12619137	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12692977	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12692979	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13017988	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13018515	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13021571	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13399316	1.00[ASW][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];0.80[LWK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs1400816	1.00[JPT][hapmap]
rs1878583	1.00[ASW][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs1982288	1.00[ASW][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs2028670	1.00[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2028671	1.00[ASW][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2028672	1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs2028673	0.80[AFR][1000 genomes]
rs2028674	0.80[AFR][1000 genomes]
rs2056202	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2138873	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2176466	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2357064	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs2357206	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2357207	0.87[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs2357208	1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs28372952	1.00[ASW][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.80[ASN][1000 genomes]
rs2884123	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3770443	1.00[JPT][hapmap]
rs3770453	0.84[ASW][hapmap];0.89[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs3770457	1.00[JPT][hapmap]
rs3791343	0.84[ASN][1000 genomes]
rs3821092	1.00[JPT][hapmap]
rs3821094	1.00[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs3821096	1.00[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs4072279	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4324292	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4668413	0.87[EUR][1000 genomes]
rs4668415	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4668416	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4668417	1.00[ASW][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs4668419	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59853867	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs60315614	0.83[AMR][1000 genomes]
rs60706248	0.87[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6433313	0.94[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs6433315	1.00[ASW][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs6433317	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6433318	1.00[ASW][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6433322	0.83[ASW][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap];0.82[YRI][hapmap]
rs6707142	1.00[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6708365	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6711813	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6714214	1.00[ASW][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6726050	0.95[AFR][1000 genomes]
rs6726991	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6727459	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6736159	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6740705	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6741030	0.90[AFR][1000 genomes]
rs6742905	0.80[ASN][1000 genomes]
rs6753551	0.83[AFR][1000 genomes]
rs6753859	0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs6757680	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6758494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6760680	0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7340516	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7371503	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7579509	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7580132	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7580232	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7588025	0.94[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7594478	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];0.98[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7597525	0.80[ASN][1000 genomes]
rs925881	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs949548	0.94[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs9636293	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs970948	0.94[ASW][hapmap];0.89[CEU][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][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	nsv875410	chr2:172693780-172896587	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv875411	chr2:172693780-172942448	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv2830399	chr2:172781830-172952526	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1443700	RAPGEF4	cis	cerebellum	SCAN
rs1443700	AC068039.4	cis	Stomach	GTEx
rs1443700	MAP1D	cis	parietal	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172780400-172848800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:172780600-172847400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr2:172780600-172854200	Weak transcription	Small Intestine	intestine
4	chr2:172783600-172851000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr2:172796000-172855200	Weak transcription	Gastric	stomach
6	chr2:172808000-172847200	Weak transcription	Fetal Brain Female	brain
7	chr2:172808000-172849400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr2:172810000-172862600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:172811800-172852200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:172811800-172855600	Weak transcription	Fetal Heart	heart
11	chr2:172813000-172859200	Weak transcription	Fetal Brain Male	brain
12	chr2:172815400-172850000	Weak transcription	HSMMtube	muscle
13	chr2:172821000-172862800	Weak transcription	Brain Angular Gyrus	brain
14	chr2:172823000-172850400	Weak transcription	Right Ventricle	heart
15	chr2:172823800-172851200	Weak transcription	Fetal Kidney	kidney
16	chr2:172824000-172857800	Weak transcription	Brain Anterior Caudate	brain
17	chr2:172824000-172857800	Weak transcription	Brain Hippocampus Middle	brain
18	chr2:172824200-172850000	Weak transcription	NHDF-Ad	bronchial
19	chr2:172824200-172850400	Weak transcription	HMEC	breast
20	chr2:172824400-172847200	Weak transcription	NH-A	brain
21	chr2:172825800-172846400	Weak transcription	Colon Smooth Muscle	Colon
22	chr2:172826400-172848400	Weak transcription	Hela-S3	cervix
23	chr2:172829200-172847000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr2:172829800-172848000	Weak transcription	HUVEC	blood vessel
25	chr2:172835800-172850200	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr2:172836200-172851000	Strong transcription	Dnd41	blood
27	chr2:172836400-172849200	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr2:172836400-172851000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr2:172838800-172849200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr2:172839200-172849000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr2:172839200-172849800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:172839800-172848200	Strong transcription	Fetal Muscle Trunk	muscle
33	chr2:172840000-172847600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr2:172840000-172848000	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr2:172840000-172849200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr2:172840200-172848200	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr2:172840200-172849000	Strong transcription	Liver	Liver
38	chr2:172840200-172849400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr2:172840600-172846400	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr2:172840600-172848400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr2:172840600-172849000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr2:172840800-172857600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:172841000-172847000	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr2:172841000-172849000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr2:172841000-172849000	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr2:172841000-172849200	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr2:172841000-172849400	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr2:172841000-172849600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr2:172841200-172846600	Strong transcription	Adipose Nuclei	Adipose
50	chr2:172841200-172847600	Strong transcription	HepG2	liver

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