Variant report

Variant	rs2631731
Chromosome Location	chr4:8429817-8429818
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:8416707..8419298-chr4:8428396..8430193,3	MCF-7	breast:
2	chr4:8428067..8433323-chr4:8440948..8445760,8	K562	blood:
3	chr4:8429725..8430462-chrX:12992795..12993539,2	HCT-116	colon:
4	chr4:8414211..8417979-chr4:8429248..8432423,3	MCF-7	breast:
5	chr4:8428810..8430394-chr4:8440724..8444143,3	K562	blood:
6	chr4:8429704..8431761-chr4:8439023..8440743,2	MCF-7	breast:
7	chr4:8429518..8431924-chr4:8437588..8440150,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155275	Chromatin interaction
ENSG00000087008	Chromatin interaction
ENSG00000205542	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10461079	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1357481	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1543246	0.82[ASN][1000 genomes]
rs1880023	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1880024	1.00[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1916326	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1949733	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2010758	0.87[ASN][1000 genomes]
rs2140337	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2255501	0.84[EUR][1000 genomes]
rs2386227	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2450475	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2631734	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2631735	0.88[MKK][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap]
rs2631736	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2631740	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2631742	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2631743	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2631744	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2631745	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2631746	0.87[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2631754	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2631756	0.85[AMR][1000 genomes]
rs2631758	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2631762	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2688219	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2688223	0.95[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2688224	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2688227	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2688231	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2688233	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2688235	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2688242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2688243	1.00[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2688247	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3103067	0.95[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3103069	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3103070	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3103071	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3103072	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3103099	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4696828	1.00[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6447875	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6837429	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6845969	0.90[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6858542	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs868105	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs871768	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs940133	0.95[CEU][hapmap];0.89[YRI][hapmap];0.95[EUR][1000 genomes]
rs940134	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs940136	1.00[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002794	chr4:8110083-8490934	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv878601	chr4:8214767-8440951	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv878602	chr4:8214767-8448992	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv878604	chr4:8315938-8618916	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv1002680	chr4:8357163-8721214	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv461220	chr4:8372944-8458394	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv593638	chr4:8372944-8458394	Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv470014	chr4:8390646-8429817	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
9	nsv829854	chr4:8402921-8506407	Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv964028	chr4:8418957-8430160	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	esv3439603	chr4:8428877-8431425	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2631731	ACOX3	Cis_1M	lymphoblastoid	RTeQTL
rs2631731	GPR78	cis	parietal	SCAN
rs2631731	TBC1D14	cis	parietal	SCAN
rs2631731	ACOX3	cis	lymphoblastoid	seeQTL
rs2631731	RP11-689P11.2	cis	lung	GTEx
rs2631731	EVC	cis	parietal	SCAN
rs2631731	C4orf23	cis	parietal	SCAN
rs2631731	C4orf23	cis	cerebellum	SCAN
rs2631731	TRMT44	cis	Nerve Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8428200-8431200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr4:8428800-8430000	Active TSS	Right Atrium	heart
3	chr4:8429000-8430000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
4	chr4:8429000-8430400	Active TSS	NHDF-Ad	bronchial
5	chr4:8429000-8431000	Active TSS	Hela-S3	cervix
6	chr4:8429200-8430400	Active TSS	Psoas Muscle	Psoas
7	chr4:8429200-8430400	Active TSS	Rectal Smooth Muscle	rectum
8	chr4:8429200-8430600	Active TSS	Aorta	Aorta
9	chr4:8429200-8430800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr4:8429200-8430800	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr4:8429200-8430800	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr4:8429200-8430800	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr4:8429200-8430800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr4:8429200-8431000	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr4:8429200-8431000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr4:8429200-8431000	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr4:8429200-8431000	Active TSS	HepG2	liver
18	chr4:8429400-8430000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
19	chr4:8429400-8430200	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr4:8429400-8430400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr4:8429400-8430400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr4:8429400-8430400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr4:8429400-8430400	Active TSS	Fetal Heart	heart
24	chr4:8429400-8430400	Active TSS	Pancreas	Pancrea
25	chr4:8429400-8430600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr4:8429400-8430600	Active TSS	Colon Smooth Muscle	Colon
27	chr4:8429400-8430600	Active TSS	Fetal Intestine Large	intestine
28	chr4:8429400-8430800	Active TSS	iPS-18 Cell Line	embryonic stem cell
29	chr4:8429400-8430800	Flanking Active TSS	Primary B cells from cord blood	blood
30	chr4:8429400-8430800	Active TSS	A549	lung
31	chr4:8429400-8431000	Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr4:8429400-8431000	Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr4:8429400-8431000	Flanking Active TSS	Primary hematopoietic stem cells	blood
34	chr4:8429600-8430000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr4:8429600-8430200	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
36	chr4:8429600-8430200	Active TSS	Lung	lung
37	chr4:8429600-8430200	Active TSS	Small Intestine	intestine
38	chr4:8429600-8430400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr4:8429600-8430400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr4:8429600-8430400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
41	chr4:8429600-8430400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr4:8429600-8430400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr4:8429600-8430400	Active TSS	Brain Hippocampus Middle	brain
44	chr4:8429600-8430400	Active TSS	Brain Substantia Nigra	brain
45	chr4:8429600-8430400	Active TSS	HSMM	muscle
46	chr4:8429600-8430600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
47	chr4:8429600-8430600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr4:8429600-8430600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr4:8429600-8430600	Active TSS	Esophagus	oesophagus
50	chr4:8429600-8430600	Active TSS	Left Ventricle	heart

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