Variant report

Variant	rs1342542
Chromosome Location	chr9:3476260-3476261
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:3472148..3476426-chr9:3525120..3528323,5	MCF-7	breast:
2	chr9:3474241..3476726-chr9:3530164..3531864,2	K562	blood:
3	chr9:3474071..3478012-chr9:3525066..3526947,3	K562	blood:
4	chr9:3474527..3477268-chr9:3526312..3529776,3	K562	blood:

Variant related genes	Relation type
ENSG00000232104	Chromatin interaction
ENSG00000080298	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10113926	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10114162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10114838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10115088	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs10115578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10117292	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10119475	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10119982	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10121096	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10123122	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10123592	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10124613	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10758273	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10758286	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10814148	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10814189	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10814190	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs10814208	0.87[CEU][hapmap];0.95[JPT][hapmap]
rs10814233	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs10972184	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10972200	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10972435	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs12004862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12238307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12340274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12353393	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12553270	0.87[CEU][hapmap];0.83[CHB][hapmap]
rs2027089	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs7022948	0.87[CEU][hapmap];0.81[JPT][hapmap]
rs7026025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7027858	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7027862	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs7037463	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7041399	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs7857554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7861625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7871777	0.87[CEU][hapmap];0.90[JPT][hapmap]
rs881167	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032921	chr9:3139007-3502815	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv539940	chr9:3139007-3502815	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv531566	chr9:3288211-3545454	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv892089	chr9:3290569-3578094	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv916259	chr9:3308176-4296711	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv1034280	chr9:3319718-3491987	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv539942	chr9:3319718-3491987	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1028815	chr9:3319718-3584455	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
9	nsv892090	chr9:3391364-3496660	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1019324	chr9:3436845-3502815	ZNF genes & repeats Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv1022795	chr9:3436845-3744623	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
12	nsv892091	chr9:3459635-3508284	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3447400-3478800	Weak transcription	Aorta	Aorta
2	chr9:3455000-3483000	Weak transcription	Fetal Thymus	thymus
3	chr9:3467600-3478600	Weak transcription	Left Ventricle	heart
4	chr9:3468000-3477200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr9:3468000-3480800	Weak transcription	NHDF-Ad	bronchial
6	chr9:3468200-3476400	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr9:3468200-3482200	Weak transcription	A549	lung
8	chr9:3468600-3477200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr9:3468600-3477400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr9:3468600-3478600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr9:3468600-3480200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr9:3468600-3483800	Weak transcription	Brain Hippocampus Middle	brain
13	chr9:3468600-3484800	Weak transcription	Ovary	ovary
14	chr9:3468800-3496600	Weak transcription	HSMMtube	muscle
15	chr9:3469000-3478600	Weak transcription	Brain Germinal Matrix	brain
16	chr9:3469000-3478800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr9:3469200-3478400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr9:3469200-3478600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr9:3469400-3495600	Weak transcription	Fetal Kidney	kidney
20	chr9:3469800-3477800	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr9:3470200-3476400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr9:3471000-3480600	Enhancers	HUVEC	blood vessel
23	chr9:3471800-3477600	Weak transcription	Fetal Brain Female	brain
24	chr9:3472000-3478600	Weak transcription	Fetal Lung	lung
25	chr9:3472000-3480400	Weak transcription	Fetal Heart	heart
26	chr9:3472800-3476400	Enhancers	Primary B cells from peripheral blood	blood
27	chr9:3473600-3476400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr9:3473600-3477200	Weak transcription	Dnd41	blood
29	chr9:3473600-3478600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr9:3473600-3496600	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr9:3473800-3476400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr9:3473800-3482200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr9:3474000-3477400	Weak transcription	Primary hematopoietic stem cells	blood
34	chr9:3474000-3493600	Weak transcription	Fetal Stomach	stomach
35	chr9:3474200-3477200	Weak transcription	Primary T cells from cord blood	blood
36	chr9:3474200-3477400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr9:3474400-3477600	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr9:3474400-3490800	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr9:3474400-3524400	Weak transcription	Thymus	Thymus
40	chr9:3474600-3486000	Weak transcription	Small Intestine	intestine
41	chr9:3474800-3477200	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr9:3475000-3477000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr9:3475000-3492600	Weak transcription	Lung	lung
44	chr9:3475400-3476400	Enhancers	Primary T cells fromperipheralblood	blood
45	chr9:3475600-3476600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr9:3475600-3480200	Weak transcription	Pancreas	Pancrea
47	chr9:3475800-3476400	Strong transcription	Primary B cells from cord blood	blood
48	chr9:3475800-3477400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr9:3475800-3478400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr9:3475800-3480000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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