Variant report

Variant	rs6737429
Chromosome Location	chr2:97028762-97028763
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:97028628..97030258-chr2:97173835..97175488,2	MCF-7	breast:
2	chr2:97022665..97024722-chr2:97027566..97029365,2	K562	blood:
3	chr2:97027281..97029651-chr2:97031268..97034024,2	K562	blood:

Variant related genes	Relation type
ENSG00000163121	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1044594	0.83[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap]
rs1048675	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11551400	0.91[ASW][hapmap];0.88[YRI][hapmap]
rs11903461	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12614188	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17420101	0.83[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap]
rs17479466	0.92[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs17633463	0.87[CEU][hapmap];0.81[AMR][1000 genomes]
rs2085842	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2276648	0.81[AMR][1000 genomes]
rs2276649	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.87[YRI][hapmap];0.84[EUR][1000 genomes]
rs2279105	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.85[EUR][1000 genomes]
rs2305935	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3171927	0.88[GIH][hapmap];0.87[TSI][hapmap]
rs3214058	0.92[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs3214063	0.92[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs3731930	0.92[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap]
rs3731935	0.80[CEU][hapmap];0.90[GIH][hapmap];0.82[TSI][hapmap]
rs4907233	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4907307	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs4907310	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4907311	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4907312	0.92[CEU][hapmap];0.95[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56027554	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56221936	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57406815	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58328293	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59966106	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs59979953	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62153915	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62153923	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62154786	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62154787	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6755877	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7562544	0.92[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv874679	chr2:96860971-97184160	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
8	nsv508155	chr2:96934695-97138302	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs6737429	AC008268.2	cis	Whole Blood	GTEx
rs6737429	AC008268.2	cis	Nerve Tibial	GTEx
rs6737429	AC008268.2	cis	Muscle Skeletal	GTEx
rs6737429	MGAT4A	cis	parietal	SCAN
rs6737429	CIAO1	cis	lymphoblastoid	seeQTL
rs6737429	AC008268.2	cis	Artery Tibial	GTEx
rs6737429	AC008268.2	cis	Artery Aorta	GTEx
rs6737429	CIAO1	cis	Skin Sun Exposed Lower leg	GTEx
rs6737429	CIAO1	cis	Adipose Subcutaneous	GTEx
rs6737429	TEKT4	cis	cerebellum	SCAN
rs6737429	CIAO1	Cis_1M	lymphoblastoid	RTeQTL
rs6737429	CIAO1	cis	Whole Blood	GTEx
rs6737429	AC008268.2	cis	lung	GTEx
rs6737429	AC008268.2	cis	Skin Sun Exposed Lower leg	GTEx
rs6737429	AC008268.2	cis	Adipose Subcutaneous	GTEx
rs6737429	CIAO1	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97002000-97036000	Weak transcription	Gastric	stomach
2	chr2:97002200-97037600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:97002600-97031600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr2:97002800-97040000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:97003200-97031400	Weak transcription	Primary B cells from cord blood	blood
6	chr2:97004000-97040400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:97004200-97040400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr2:97006200-97041000	Strong transcription	Dnd41	blood
9	chr2:97006600-97040200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:97006600-97040400	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr2:97006800-97040400	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr2:97006800-97040600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr2:97006800-97040800	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr2:97007000-97040600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:97007200-97040000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr2:97007200-97040200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr2:97007200-97040400	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr2:97007200-97041600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr2:97007400-97040200	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr2:97007400-97040400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr2:97007400-97040600	Strong transcription	Thymus	Thymus
22	chr2:97008400-97033600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr2:97011200-97038000	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr2:97011400-97038400	Strong transcription	GM12878-XiMat	blood
25	chr2:97012400-97037600	Weak transcription	Colonic Mucosa	Colon
26	chr2:97012600-97035600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr2:97012600-97040000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr2:97013800-97040000	Weak transcription	Esophagus	oesophagus
29	chr2:97014800-97040600	Strong transcription	A549	lung
30	chr2:97015000-97039600	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr2:97016800-97035800	Weak transcription	Brain Germinal Matrix	brain
32	chr2:97017000-97040000	Weak transcription	Fetal Kidney	kidney
33	chr2:97017800-97030800	Weak transcription	Fetal Brain Female	brain
34	chr2:97018200-97028800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
35	chr2:97019200-97035000	Weak transcription	Placenta	Placenta
36	chr2:97019200-97040600	Strong transcription	Fetal Thymus	thymus
37	chr2:97019200-97042000	Weak transcription	Spleen	Spleen
38	chr2:97019400-97033600	Strong transcription	K562	blood
39	chr2:97020000-97030000	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr2:97020000-97033000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr2:97020000-97039200	Weak transcription	Fetal Heart	heart
42	chr2:97020000-97041400	Weak transcription	HSMM	muscle
43	chr2:97020200-97035600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr2:97020200-97037000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr2:97020600-97031400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr2:97020800-97029400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr2:97022600-97029400	Weak transcription	Fetal Intestine Large	intestine
48	chr2:97024000-97029400	Weak transcription	Primary hematopoietic stem cells	blood
49	chr2:97024400-97033600	Strong transcription	Fetal Stomach	stomach
50	chr2:97024400-97040000	Strong transcription	HUES48 Cell Line	embryonic stem cell

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