Variant report

Variant	rs4744201
Chromosome Location	chr9:96015256-96015257
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:96005639..96009586-chr9:96012508..96016680,4	MCF-7	breast:
2	chr10:74025928..74028386-chr9:96014931..96017189,2	MCF-7	breast:
3	chr9:96014587..96017467-chr9:96024628..96027313,2	K562	blood:

Variant related genes	Relation type
ENSG00000165238	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10761203	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821080	1.00[CEU][hapmap];0.91[MEX][hapmap]
rs10821086	0.92[CEU][hapmap];0.83[MEX][hapmap]
rs10821088	1.00[CEU][hapmap]
rs10821095	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10821098	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10992698	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10992702	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12336667	1.00[CEU][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs12341303	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12684394	0.96[ASN][1000 genomes]
rs1317698	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13292831	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13293217	0.84[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.87[ASN][1000 genomes]
rs1544229	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16936753	0.82[JPT][hapmap]
rs2040093	0.92[CEU][hapmap]
rs2040094	0.92[CEU][hapmap]
rs2086103	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2306183	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2398822	0.95[ASN][1000 genomes]
rs3001450	0.81[ASN][1000 genomes]
rs3001451	0.81[ASN][1000 genomes]
rs35795732	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3763634	1.00[CHB][hapmap];0.98[ASN][1000 genomes]
rs3763635	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3793546	0.94[ASN][1000 genomes]
rs4743911	0.92[CEU][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4744192	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4744195	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4744203	0.84[ASN][1000 genomes]
rs4744206	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4744212	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]
rs4744215	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7846729	0.85[CEU][hapmap]
rs7857039	0.91[CEU][hapmap]
rs7857937	0.92[CEU][hapmap];0.83[MEX][hapmap]
rs7868971	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs944993	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[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	nsv526296	chr9:95708192-96030392	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers 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	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
3	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
4	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
5	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
6	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
7	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:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95995200-96026400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr9:95995600-96030600	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr9:96001800-96018800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr9:96002600-96016400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr9:96005400-96033800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr9:96005600-96026200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr9:96006200-96043800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:96007000-96020400	Weak transcription	Fetal Muscle Leg	muscle
9	chr9:96008000-96030200	Strong transcription	Fetal Intestine Small	intestine
10	chr9:96008000-96030400	Strong transcription	Fetal Intestine Large	intestine
11	chr9:96008200-96026600	Weak transcription	Spleen	Spleen
12	chr9:96008200-96027600	Weak transcription	Right Atrium	heart
13	chr9:96008400-96016600	Weak transcription	Gastric	stomach
14	chr9:96008800-96017200	Weak transcription	Brain Angular Gyrus	brain
15	chr9:96008800-96026200	Weak transcription	Placenta	Placenta
16	chr9:96010600-96016600	Weak transcription	Colonic Mucosa	Colon
17	chr9:96011000-96016600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr9:96011000-96026400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr9:96011200-96017000	Weak transcription	Brain Anterior Caudate	brain
20	chr9:96011200-96017400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr9:96011200-96017600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr9:96011200-96018600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr9:96011200-96019400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr9:96011200-96030600	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr9:96011200-96032800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr9:96011200-96033400	Weak transcription	A549	lung
27	chr9:96011800-96026200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr9:96012600-96019800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr9:96012800-96032600	Weak transcription	Fetal Brain Male	brain
30	chr9:96013000-96031400	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr9:96013600-96016200	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr9:96013800-96022600	Strong transcription	Duodenum Mucosa	Duodenum
33	chr9:96014000-96033800	Strong transcription	Stomach Smooth Muscle	stomach
34	chr9:96014200-96015400	Enhancers	Brain Hippocampus Middle	brain
35	chr9:96014200-96019600	Strong transcription	HepG2	liver
36	chr9:96014400-96015400	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr9:96014400-96015400	Enhancers	Left Ventricle	heart
38	chr9:96014400-96017200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr9:96014400-96017800	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr9:96014400-96025400	Strong transcription	Brain Germinal Matrix	brain
41	chr9:96014400-96032800	Strong transcription	Fetal Brain Female	brain
42	chr9:96014600-96018600	Strong transcription	Skeletal Muscle Male	skeletal muscle
43	chr9:96014600-96019400	Weak transcription	Fetal Thymus	thymus
44	chr9:96014600-96021200	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr9:96014800-96016000	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr9:96014800-96019400	Strong transcription	Pancreas	Pancrea
47	chr9:96014800-96026800	Weak transcription	Fetal Heart	heart
48	chr9:96015000-96015800	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr9:96015000-96016600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr9:96015000-96020200	Weak transcription	Colon Smooth Muscle	Colon

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