Variant report

Variant	rs4744212
Chromosome Location	chr9:96038262-96038263
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:96036607..96039840-chr9:96048274..96051668,3	MCF-7	breast:
2	chr9:95922407..95924638-chr9:96036435..96038460,2	MCF-7	breast:
3	chr9:96034754..96037251-chr9:96038032..96040798,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165238	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10761203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10821080	0.96[CEU][hapmap]
rs10821086	0.89[CEU][hapmap]
rs10821088	0.96[CEU][hapmap]
rs10821095	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10821098	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10992698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992702	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12336667	0.96[CEU][hapmap]
rs12341303	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12684394	0.96[ASN][1000 genomes]
rs1317698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13292831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13293217	0.89[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs1544229	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16936753	0.82[JPT][hapmap]
rs2040093	0.86[CEU][hapmap]
rs2040094	0.86[CEU][hapmap]
rs2086103	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2306183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2398822	0.94[ASN][1000 genomes]
rs3001450	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3001451	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35795732	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3763634	1.00[CHB][hapmap];0.97[ASN][1000 genomes]
rs3763635	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3793546	0.93[ASN][1000 genomes]
rs4743911	0.96[CEU][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4744192	0.83[EUR][1000 genomes]
rs4744195	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4744201	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4744203	0.84[ASN][1000 genomes]
rs4744206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744215	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7857039	0.84[CEU][hapmap]
rs7857937	0.89[CEU][hapmap]
rs7868971	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs944993	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893576	chr9:95789960-96158277	Active TSS Weak transcription Enhancers Flanking Active TSS Strong 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 miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv893580	chr9:95855100-96099377	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer 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
3	nsv430082	chr9:95905745-96095045	Genic enhancers Enhancers Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv893582	chr9:95963114-96116937	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv893583	chr9:95996573-96091688	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv893584	chr9:96002983-96116937	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96006200-96043800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:96025600-96041200	Weak transcription	Psoas Muscle	Psoas
3	chr9:96027200-96051200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:96027200-96056000	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr9:96027200-96061000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr9:96031400-96054600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr9:96031400-96055000	Weak transcription	Colonic Mucosa	Colon
8	chr9:96031400-96062800	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr9:96031600-96040400	Weak transcription	HepG2	liver
10	chr9:96032600-96043400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr9:96033000-96054600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr9:96033000-96055000	Weak transcription	Brain Anterior Caudate	brain
13	chr9:96033000-96067200	Weak transcription	Brain Angular Gyrus	brain
14	chr9:96033400-96062800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr9:96033400-96067000	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr9:96033400-96077200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr9:96033600-96044400	Weak transcription	Left Ventricle	heart
18	chr9:96033600-96046000	Weak transcription	Pancreas	Pancrea
19	chr9:96033600-96050200	Weak transcription	Fetal Intestine Small	intestine
20	chr9:96033600-96054600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr9:96033600-96060200	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr9:96033600-96061000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr9:96033600-96072800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr9:96033800-96040400	Weak transcription	Stomach Smooth Muscle	stomach
25	chr9:96033800-96040600	Weak transcription	Duodenum Mucosa	Duodenum
26	chr9:96033800-96054600	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr9:96033800-96060400	Weak transcription	Colon Smooth Muscle	Colon
28	chr9:96034200-96040400	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr9:96034400-96039800	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr9:96034400-96040000	Weak transcription	Brain Germinal Matrix	brain
31	chr9:96035800-96051600	Weak transcription	Fetal Intestine Large	intestine
32	chr9:96036400-96039400	Weak transcription	Fetal Brain Female	brain
33	chr9:96036400-96039800	Weak transcription	Fetal Heart	heart
34	chr9:96036600-96042600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr9:96036800-96042600	Weak transcription	Fetal Stomach	stomach

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