Variant report

Variant	rs6426940
Chromosome Location	chr1:165733483-165733484
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:165732937..165734507-chr1:167189047..167191428,2	MCF-7	breast:
2	chr1:165731771..165733525-chr1:165736901..165738837,2	K562	blood:
3	chr1:165727367..165730301-chr1:165730558..165733503,2	MCF-7	breast:
4	chr1:165730442..165735280-chr1:165736024..165740207,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143190	Chromatin interaction
ENSG00000272205	Chromatin interaction
ENSG00000224358	Chromatin interaction
ENSG00000143183	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10800152	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs10918266	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10918276	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10918281	0.91[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs12028087	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12723198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs14223	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1913846	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2153263	0.80[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]
rs2153264	0.80[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]
rs2790057	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs2814470	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4656462	0.91[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs4657470	0.88[CEU][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs6426937	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6656194	0.81[CHB][hapmap]
rs6670705	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7411708	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7512095	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7540840	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][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	esv2756102	chr1:165652342-165877342	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1011720	chr1:165669589-165802516	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription 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	41 gene(s)	inside rSNPs	diseases
3	nsv518886	chr1:165714187-165741646	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6426940	ARHGAP30	cis	parietal	SCAN
rs6426940	ADCY10	cis	parietal	SCAN
rs6426940	FZD2	trans	brain	seeQTL
rs6426940	FCGR3A	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165687600-165737600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:165694600-165736800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr1:165711200-165736200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:165712200-165737000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:165712600-165737000	Weak transcription	Colonic Mucosa	Colon
6	chr1:165713400-165733600	Weak transcription	NHEK	skin
7	chr1:165713600-165737000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:165721800-165734800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:165721800-165734800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr1:165721800-165734800	Weak transcription	Esophagus	oesophagus
11	chr1:165721800-165735200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr1:165721800-165736600	Weak transcription	Stomach Mucosa	stomach
13	chr1:165721800-165737000	Weak transcription	Fetal Brain Male	brain
14	chr1:165721800-165737000	Weak transcription	Fetal Heart	heart
15	chr1:165721800-165737000	Weak transcription	Right Atrium	heart
16	chr1:165721800-165737200	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr1:165721800-165737600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:165722400-165735000	Weak transcription	HSMMtube	muscle
19	chr1:165722600-165733600	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr1:165722600-165736800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:165722800-165734800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr1:165723000-165736800	Weak transcription	Spleen	Spleen
23	chr1:165723200-165736800	Weak transcription	Colon Smooth Muscle	Colon
24	chr1:165723400-165734800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:165723600-165733600	Weak transcription	Brain Angular Gyrus	brain
26	chr1:165723600-165735600	Weak transcription	Brain Germinal Matrix	brain
27	chr1:165723800-165733800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:165724000-165733800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr1:165724200-165733600	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr1:165724200-165733600	Weak transcription	Brain Hippocampus Middle	brain
31	chr1:165724200-165733600	Weak transcription	HUVEC	blood vessel
32	chr1:165725200-165733600	Weak transcription	Small Intestine	intestine
33	chr1:165725800-165734200	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr1:165726400-165736800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr1:165726800-165736800	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr1:165726800-165737000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:165727000-165736800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:165727600-165734200	Weak transcription	Fetal Lung	lung
39	chr1:165727600-165735000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr1:165727600-165735000	Weak transcription	Aorta	Aorta
41	chr1:165727800-165735400	Weak transcription	Right Ventricle	heart
42	chr1:165727800-165737000	Weak transcription	Psoas Muscle	Psoas
43	chr1:165727800-165737600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr1:165728200-165733600	Weak transcription	Ovary	ovary
45	chr1:165729000-165733800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr1:165729200-165734200	Weak transcription	Fetal Kidney	kidney
47	chr1:165729200-165737200	Weak transcription	Brain Substantia Nigra	brain
48	chr1:165730000-165734000	Strong transcription	Liver	Liver
49	chr1:165730200-165736800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr1:165730200-165736800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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