Variant report

Variant	rs3731935
Chromosome Location	chr2:97020049-97020050
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:96967317..96973483-chr2:97015597..97021868,10	K562	blood:
2	chr2:97013257..97015542-chr2:97017707..97021089,3	MCF-7	breast:
3	chr2:97015565..97019421-chr2:97019712..97022858,3	MCF-7	breast:
4	chr2:96970882..96973483-chr2:97016392..97020866,5	K562	blood:
5	chr2:97017761..97020672-chr2:97030322..97032305,2	MCF-7	breast:
6	chr2:97018374..97021886-chr2:97022471..97025648,3	MCF-7	breast:
7	chr2:96931523..96934928-chr2:97018451..97020493,3	K562	blood:

Variant related genes	Relation type
ENSG00000135956	Chromatin interaction
ENSG00000144021	Chromatin interaction
ENSG00000144028	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1044594	0.88[GIH][hapmap]
rs1048675	0.80[CEU][hapmap]
rs11903461	0.80[CEU][hapmap];0.90[GIH][hapmap];0.82[TSI][hapmap]
rs17420101	0.88[GIH][hapmap]
rs17479466	0.88[GIH][hapmap]
rs17633463	0.83[CEU][hapmap]
rs2278563	0.91[MKK][hapmap]
rs2279105	0.80[CEU][hapmap];0.90[GIH][hapmap];0.82[TSI][hapmap]
rs2305935	0.90[GIH][hapmap];0.87[TSI][hapmap]
rs3171927	0.91[CEU][hapmap];0.90[CHB][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3214058	0.88[GIH][hapmap]
rs3214063	0.88[GIH][hapmap]
rs3731936	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4907231	0.84[ASN][1000 genomes]
rs4907232	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4907237	0.85[MKK][hapmap]
rs4907310	0.80[CEU][hapmap];0.90[GIH][hapmap];0.82[TSI][hapmap]
rs4907311	0.90[GIH][hapmap]
rs4907312	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap]
rs62153034	0.81[ASN][1000 genomes]
rs62153041	0.81[ASN][1000 genomes]
rs62153898	0.81[ASN][1000 genomes]
rs62153900	0.81[ASN][1000 genomes]
rs62153901	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62153902	0.81[EUR][1000 genomes]
rs62153905	0.89[ASN][1000 genomes]
rs62153906	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62153915	0.86[ASN][1000 genomes]
rs62153917	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs62153922	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6737429	0.80[CEU][hapmap];0.90[GIH][hapmap];0.82[TSI][hapmap]
rs7562544	0.87[CEU][hapmap];0.90[CHB][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.88[MKK][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]

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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3731935	AC008268.2	cis	Artery Tibial	GTEx
rs3731935	CIAO1	cis	Liver	GTEx
rs3731935	AC008268.2	cis	Whole Blood	GTEx
rs3731935	AC008268.2	cis	Skin Sun Exposed Lower leg	GTEx
rs3731935	AC008268.2	cis	Adipose Subcutaneous	GTEx
rs3731935	CIAO1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:99 , 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	chr2:97007200-97023000	Strong transcription	H9 Cell Line	embryonic stem cell
16	chr2:97007200-97023400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr2:97007200-97024000	Strong transcription	Fetal Stomach	stomach
18	chr2:97007200-97040000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr2:97007200-97040200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr2:97007200-97040400	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr2:97007200-97041600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:97007400-97020400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr2:97007400-97023200	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr2:97007400-97023600	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr2:97007400-97040200	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr2:97007400-97040400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr2:97007400-97040600	Strong transcription	Thymus	Thymus
28	chr2:97008400-97022800	Strong transcription	HepG2	liver
29	chr2:97008400-97033600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr2:97011000-97022600	Weak transcription	Fetal Lung	lung
31	chr2:97011200-97038000	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr2:97011400-97038400	Strong transcription	GM12878-XiMat	blood
33	chr2:97011600-97024800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr2:97011600-97024800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr2:97011800-97023400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr2:97012400-97037600	Weak transcription	Colonic Mucosa	Colon
37	chr2:97012600-97035600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr2:97012600-97040000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr2:97013800-97040000	Weak transcription	Esophagus	oesophagus
40	chr2:97014400-97023000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr2:97014800-97023000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr2:97014800-97040600	Strong transcription	A549	lung
43	chr2:97015000-97039600	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr2:97015400-97021000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:97015400-97021000	Strong transcription	Primary hematopoietic stem cells	blood
46	chr2:97015400-97022000	Strong transcription	HMEC	breast
47	chr2:97015400-97023000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
48	chr2:97015600-97022600	Strong transcription	Fetal Intestine Large	intestine
49	chr2:97015600-97023000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr2:97015800-97023400	Strong transcription	NHEK	skin

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