Variant report

Variant	rs4668387
Chromosome Location	chr2:172333295-172333296
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	chr2:172332790..172336030-chr2:172339156..172342028,3	K562	blood:
2	chr2:172327035..172329499-chr2:172331257..172333363,3	K562	blood:

Variant related genes	Relation type
ENSG00000115827	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10445722	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10445762	0.86[TSI][hapmap]
rs10490604	0.80[EUR][1000 genomes]
rs10515933	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[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];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12151641	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1558936	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17220419	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17220440	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17220608	0.93[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17220657	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17220699	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17220734	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[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];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17221346	0.96[CHD][hapmap];0.90[GIH][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs17221367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17221402	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17221619	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17286415	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17286660	1.00[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1861899	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1981788	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2111718	0.85[TSI][hapmap]
rs2160849	0.86[TSI][hapmap]
rs2356781	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28742013	0.80[EUR][1000 genomes]
rs36112363	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3731981	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3731982	0.93[CEU][hapmap];0.86[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3731983	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[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];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3731985	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3795998	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];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3821084	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];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4417688	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4458186	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4496302	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4522571	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4668385	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4668386	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56410960	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs57099324	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58536060	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59960186	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs60439518	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62181352	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs62183467	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62183468	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62183470	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs62183471	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs62183472	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62183492	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62183493	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62183494	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62183495	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62183497	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62183498	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62183499	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62183502	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62183503	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62183506	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62183507	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62183539	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6433290	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6433291	0.93[CHD][hapmap];0.90[GIH][hapmap];0.85[TSI][hapmap]
rs6433292	0.93[CEU][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6713612	0.93[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6720250	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6740733	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6741806	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6743290	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6751956	0.85[CHD][hapmap];0.90[GIH][hapmap];0.85[TSI][hapmap]
rs7562674	0.89[ASW][hapmap];0.81[LWK][hapmap];0.80[MKK][hapmap]
rs7568037	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7572334	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7576894	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7598137	1.00[ASW][hapmap];0.97[GIH][hapmap];0.84[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7606658	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9678149	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9678164	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9679537	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9789572	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];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9789596	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3382346	chr2:172062677-172363892	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	esv1832950	chr2:172283513-172488111	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4668387	DLX1	cis	cerebellum	SCAN
rs4668387	CYBRD1	Cis_1M	lymphoblastoid	RTeQTL
rs4668387	METTL8	cis	Esophagus Muscularis	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172291800-172338200	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr2:172292000-172341600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr2:172298400-172334400	Weak transcription	Small Intestine	intestine
4	chr2:172298400-172339400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:172298600-172341400	Weak transcription	NHLF	lung
6	chr2:172300600-172338600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr2:172304800-172338800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr2:172306000-172348000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr2:172306800-172334000	Weak transcription	Psoas Muscle	Psoas
10	chr2:172307800-172341200	Weak transcription	Right Ventricle	heart
11	chr2:172309600-172348400	Weak transcription	Fetal Heart	heart
12	chr2:172313400-172339800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr2:172315000-172337400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr2:172322800-172337800	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr2:172324400-172340600	Strong transcription	Primary B cells from peripheral blood	blood
16	chr2:172324600-172338200	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr2:172324600-172340000	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr2:172324800-172334800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr2:172324800-172334800	Strong transcription	Dnd41	blood
20	chr2:172324800-172337800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr2:172324800-172340400	Strong transcription	Primary T cells from cord blood	blood
22	chr2:172324800-172341200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:172325000-172340200	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr2:172325200-172334800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr2:172325200-172335200	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr2:172325200-172338000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr2:172325200-172338600	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr2:172325200-172340000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr2:172325400-172333400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr2:172325400-172334800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr2:172325600-172334600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr2:172327000-172339600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr2:172327000-172346800	Weak transcription	Colonic Mucosa	Colon
34	chr2:172327200-172334000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr2:172327200-172334000	Weak transcription	Esophagus	oesophagus
36	chr2:172327200-172334600	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr2:172327200-172338600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr2:172327200-172339200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:172327200-172339400	Weak transcription	Pancreas	Pancrea
40	chr2:172327200-172341200	Weak transcription	Rectal Smooth Muscle	rectum
41	chr2:172327200-172341600	Weak transcription	Brain Germinal Matrix	brain
42	chr2:172327200-172344000	Weak transcription	Gastric	stomach
43	chr2:172327200-172346600	Weak transcription	Thymus	Thymus
44	chr2:172327200-172348800	Weak transcription	Spleen	Spleen
45	chr2:172327400-172333800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr2:172327400-172334000	Weak transcription	Aorta	Aorta
47	chr2:172327400-172334200	Weak transcription	HUVEC	blood vessel
48	chr2:172327400-172337400	Weak transcription	Brain Substantia Nigra	brain
49	chr2:172327400-172339400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr2:172327400-172340800	Weak transcription	Lung	lung

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