Variant report

Variant	rs2688234
Chromosome Location	chr4:8447205-8447206
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:8421637..8423534-chr4:8447080..8448932,2	K562	blood:
2	chr4:8445521..8448213-chr4:8465015..8467213,2	K562	blood:
3	chr4:8444925..8447742-chr4:8450558..8453133,4	K562	blood:
4	chr4:8442271..8445405-chr4:8446237..8450088,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000087008	Chromatin interaction
ENSG00000155275	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11729265	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12503034	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1880025	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2002860	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2049302	0.95[ASN][1000 genomes]
rs2140336	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2245515	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2245808	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2245809	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2386223	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2631723	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2631724	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2631727	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2631728	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2631729	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2631730	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2631733	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2631737	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2631750	0.81[AMR][1000 genomes]
rs2631752	0.89[ASN][1000 genomes]
rs2631757	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2631763	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2631764	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2631765	0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2631766	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2631767	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2631769	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2688221	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2688228	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2688229	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2688230	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2688239	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2688240	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2688244	0.98[ASN][1000 genomes]
rs2688246	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3103090	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3103098	0.82[CEU][hapmap];0.86[JPT][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs3115396	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3775893	0.85[EUR][1000 genomes]
rs4325994	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56343159	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs954270	0.89[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs954271	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][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	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	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
3	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
4	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
5	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
6	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
7	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2688234	ACOX3	cis	parietal	SCAN
rs2688234	C4orf23	cis	cerebellum	SCAN
rs2688234	ACOX3	cis	lymphoblastoid	seeQTL
rs2688234	TBC1D14	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8443600-8447800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr4:8443600-8455400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:8443800-8447800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr4:8443800-8449000	Weak transcription	Lung	lung
5	chr4:8444000-8447400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr4:8444000-8447800	Weak transcription	Fetal Kidney	kidney
7	chr4:8444000-8449400	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr4:8444000-8450400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr4:8444000-8452800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr4:8444200-8447600	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr4:8444200-8448000	Weak transcription	NHLF	lung
12	chr4:8444200-8456800	Weak transcription	A549	lung
13	chr4:8444400-8448400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr4:8444400-8449200	Weak transcription	Colonic Mucosa	Colon
15	chr4:8444400-8452400	Weak transcription	Primary hematopoietic stem cells	blood
16	chr4:8444400-8455400	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr4:8444600-8447400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr4:8444600-8448200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr4:8444600-8449400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr4:8444600-8452800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr4:8444600-8455800	Weak transcription	NHDF-Ad	bronchial
22	chr4:8444800-8447800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr4:8444800-8447800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr4:8444800-8447800	Weak transcription	Esophagus	oesophagus
25	chr4:8444800-8447800	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr4:8444800-8448000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr4:8444800-8448200	Weak transcription	Aorta	Aorta
28	chr4:8444800-8449200	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr4:8444800-8449800	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr4:8444800-8452600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr4:8444800-8452600	Weak transcription	HUVEC	blood vessel
32	chr4:8444800-8453400	Weak transcription	Fetal Brain Male	brain
33	chr4:8444800-8458400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr4:8445000-8447600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr4:8445000-8447800	Weak transcription	Brain Cingulate Gyrus	brain
36	chr4:8445000-8448000	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr4:8445000-8448000	Weak transcription	Spleen	Spleen
38	chr4:8445000-8448000	Weak transcription	Osteobl	bone
39	chr4:8445000-8448200	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr4:8445000-8448200	Weak transcription	Fetal Lung	lung
41	chr4:8445000-8449200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr4:8445000-8449600	Weak transcription	Fetal Thymus	thymus
43	chr4:8445000-8451000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr4:8445000-8452200	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr4:8445000-8454600	Weak transcription	NH-A	brain
46	chr4:8445000-8454800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr4:8445000-8460800	Weak transcription	Psoas Muscle	Psoas
48	chr4:8445200-8447400	Weak transcription	Primary T cells from cord blood	blood
49	chr4:8445200-8447800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr4:8445200-8447800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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