Variant report

Variant	rs6658724
Chromosome Location	chr1:224016520-224016521
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:223989181..223990826-chr1:224014851..224016646,2	K562	blood:
2	chr1:223999352..224002189-chr1:224016108..224019082,3	K562	blood:
3	chr1:223984174..223985831-chr1:224015824..224018657,2	K562	blood:

Variant related genes	Relation type
ENSG00000143514	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1003061	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1153928	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1153937	0.85[ASN][1000 genomes]
rs1153938	0.85[ASN][1000 genomes]
rs1153943	0.88[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs1153944	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1153946	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1153950	0.91[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1153952	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1153954	0.91[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1153956	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1222081	1.00[CEU][hapmap];0.94[JPT][hapmap];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1222123	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1222126	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1222127	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1222147	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1222148	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1222153	0.94[CHB][hapmap];0.83[GIH][hapmap];0.84[MEX][hapmap];0.84[AMR][1000 genomes]
rs1222158	0.94[ASW][hapmap];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[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1228475	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1538140	0.83[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.89[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17739	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1982611	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60739082	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6604726	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6661816	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6667215	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6694471	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6698919	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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs898878	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv1008800	chr1:223904653-224061032	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6658724	HLX	cis	parietal	SCAN
rs6658724	DEGS1	cis	lymphoblastoid	seeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223960200-224025400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:224002000-224023800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:224002200-224020200	Weak transcription	Placenta	Placenta
4	chr1:224002200-224020200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr1:224007000-224024000	Weak transcription	Fetal Intestine Small	intestine
6	chr1:224007800-224020200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr1:224008000-224017000	Weak transcription	Fetal Kidney	kidney
8	chr1:224008000-224019800	Weak transcription	Brain Germinal Matrix	brain
9	chr1:224008200-224019400	Weak transcription	Hela-S3	cervix
10	chr1:224008600-224019400	Weak transcription	A549	lung
11	chr1:224008800-224020200	Weak transcription	Fetal Muscle Trunk	muscle
12	chr1:224009000-224018800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:224009000-224019400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:224009000-224019400	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr1:224009000-224020400	Weak transcription	Fetal Muscle Leg	muscle
16	chr1:224009200-224019600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr1:224009200-224020400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:224009400-224019400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr1:224009400-224019800	Weak transcription	HSMM	muscle
20	chr1:224009400-224019800	Weak transcription	NHDF-Ad	bronchial
21	chr1:224009400-224020200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:224009400-224023800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr1:224010200-224026400	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr1:224011000-224020200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:224011200-224019400	Weak transcription	NH-A	brain
26	chr1:224011200-224019400	Weak transcription	Osteobl	bone
27	chr1:224011400-224019600	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr1:224013400-224017200	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr1:224013800-224019400	Weak transcription	Fetal Lung	lung
30	chr1:224013800-224019400	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr1:224013800-224021600	Weak transcription	Ovary	ovary
32	chr1:224014000-224019400	Weak transcription	Brain Anterior Caudate	brain
33	chr1:224014000-224019400	Weak transcription	Brain Hippocampus Middle	brain
34	chr1:224014000-224019800	Weak transcription	Adipose Nuclei	Adipose
35	chr1:224014000-224020200	Weak transcription	Liver	Liver
36	chr1:224014000-224020200	Weak transcription	Esophagus	oesophagus
37	chr1:224014200-224019400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr1:224014200-224019800	Weak transcription	Primary B cells from peripheral blood	blood
39	chr1:224014200-224019800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr1:224014200-224020200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr1:224014200-224020200	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr1:224014200-224020400	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr1:224014200-224021400	Weak transcription	Duodenum Mucosa	Duodenum
44	chr1:224014200-224023400	Weak transcription	Thymus	Thymus
45	chr1:224014200-224023400	Weak transcription	Dnd41	blood
46	chr1:224014200-224024400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:224014400-224016800	Genic enhancers	K562	blood
48	chr1:224014400-224018000	Enhancers	Primary neutrophils fromperipheralblood	blood
49	chr1:224014400-224020400	Weak transcription	Fetal Thymus	thymus
50	chr1:224014600-224019600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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