Variant report

Variant	rs4689059
Chromosome Location	chr4:6947570-6947571
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:6910492..6915918-chr4:6946437..6950272,7	K562	blood:
2	chr4:6918951..6920987-chr4:6946551..6948090,2	K562	blood:
3	chr4:6917668..6920987-chr4:6945472..6948090,3	K562	blood:
4	chr4:6927493..6929739-chr4:6946981..6949624,2	K562	blood:
5	chr4:6909142..6912159-chr4:6946034..6948699,3	K562	blood:

Variant related genes	Relation type
ENSG00000132405	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10012590	1.00[CHD][hapmap]
rs1048009	0.81[LWK][hapmap]
rs10516181	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs10937772	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10937774	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10937776	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs11732898	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11934364	1.00[CHB][hapmap]
rs12510715	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[ASN][1000 genomes]
rs12642852	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13108082	0.83[ASN][1000 genomes]
rs13111887	0.83[ASN][1000 genomes]
rs13122119	0.83[CHD][hapmap]
rs13135912	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2301818	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs2301819	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs2359194	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs3188939	1.00[CHD][hapmap]
rs34219101	0.83[ASN][1000 genomes]
rs3857171	0.81[AFR][1000 genomes]
rs3892490	0.83[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4234788	0.83[ASN][1000 genomes]
rs4296677	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4428285	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4458452	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4645214	1.00[CEU][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4689060	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4689566	0.89[ASN][1000 genomes]
rs4689567	0.89[ASN][1000 genomes]
rs4689568	0.85[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4689573	0.82[AMR][1000 genomes]
rs55822670	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6816660	0.83[ASN][1000 genomes]
rs6816882	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6831129	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6854776	1.00[CHD][hapmap]
rs7655563	0.85[CEU][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7658198	0.95[CEU][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7661462	0.95[CEU][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7675524	1.00[CHD][hapmap];0.89[ASN][1000 genomes]
rs7693321	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8180337	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9291126	1.00[CHB][hapmap];0.85[CHD][hapmap]

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	nsv878529	chr4:6883012-6983677	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv878530	chr4:6888932-7058473	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4689059	HMX1	cis	parietal	SCAN
rs4689059	GRPEL1	cis	lymphoblastoid	seeQTL

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:6928000-6969600	Weak transcription	Aorta	Aorta
2	chr4:6939200-6948000	Enhancers	H1 Cell Line	embryonic stem cell
3	chr4:6941800-6947800	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr4:6942000-6948000	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr4:6943800-6955400	Weak transcription	Brain Substantia Nigra	brain
6	chr4:6944400-6949800	Weak transcription	Fetal Lung	lung
7	chr4:6944600-6947800	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr4:6944800-6955400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr4:6945000-6949000	Genic enhancers	Fetal Intestine Small	intestine
10	chr4:6945000-6949600	Weak transcription	Fetal Kidney	kidney
11	chr4:6945000-6955400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr4:6945000-6970200	Weak transcription	Hela-S3	cervix
13	chr4:6945200-6955600	Weak transcription	Fetal Brain Female	brain
14	chr4:6945400-6953600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr4:6945400-6955400	Weak transcription	Fetal Stomach	stomach
16	chr4:6945600-6949800	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr4:6945600-6952800	Weak transcription	Esophagus	oesophagus
18	chr4:6945600-6952800	Weak transcription	K562	blood
19	chr4:6945600-6953000	Weak transcription	Primary B cells from peripheral blood	blood
20	chr4:6945600-6953600	Weak transcription	GM12878-XiMat	blood
21	chr4:6945600-6955600	Weak transcription	Left Ventricle	heart
22	chr4:6945800-6953600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr4:6945800-6965800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr4:6946000-6949800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr4:6946000-6953000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr4:6946400-6955400	Weak transcription	NHLF	lung
27	chr4:6946600-6949000	Weak transcription	Fetal Muscle Trunk	muscle
28	chr4:6946600-6949600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr4:6946600-6953000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr4:6946600-6955200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr4:6946600-6955400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr4:6946600-6955800	Weak transcription	Fetal Brain Male	brain
33	chr4:6946600-6969000	Weak transcription	Dnd41	blood
34	chr4:6946800-6947800	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr4:6946800-6949400	Weak transcription	Lung	lung
36	chr4:6946800-6949600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr4:6946800-6949600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr4:6946800-6949600	Weak transcription	Liver	Liver
39	chr4:6946800-6949600	Weak transcription	Gastric	stomach
40	chr4:6946800-6949600	Weak transcription	Pancreas	Pancrea
41	chr4:6946800-6952600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr4:6946800-6953600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr4:6946800-6953600	Weak transcription	Brain Hippocampus Middle	brain
44	chr4:6946800-6953600	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr4:6946800-6954000	Weak transcription	Primary B cells from cord blood	blood
46	chr4:6946800-6955400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr4:6946800-6955400	Weak transcription	Stomach Mucosa	stomach
48	chr4:6946800-6955400	Weak transcription	NHDF-Ad	bronchial
49	chr4:6947000-6947800	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr4:6947000-6947800	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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