Variant report

Variant	rs12336667
Chromosome Location	chr9:95962890-95962891
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:95961715..95963254-chr9:96067658..96070584,2	MCF-7	breast:
2	chr9:95960782..95962974-chr9:95969485..95971200,2	MCF-7	breast:
3	chr9:95961109..95963310-chr9:96212706..96215085,3	MCF-7	breast:
4	chr9:95961414..95965641-chr9:95984083..95987391,7	MCF-7	breast:
5	chr9:95957079..95960371-chr9:95962427..95964398,3	K562	blood:
6	chr9:95944881..95947924-chr9:95961775..95965090,3	MCF-7	breast:
7	chr9:95961633..95964476-chr9:96008257..96009882,2	MCF-7	breast:
8	chr9:95962461..95964580-chr9:96059375..96061154,2	MCF-7	breast:
9	chr9:95958543..95960767-chr9:95962228..95964841,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000165238	Chromatin interaction
ENSG00000048828	Chromatin interaction
ENSG00000188938	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10761203	0.96[CEU][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs10821080	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10821084	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap];0.94[ASN][1000 genomes]
rs10821086	0.92[CEU][hapmap];0.83[CHB][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10821088	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10821089	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs10821090	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs10821095	1.00[CEU][hapmap]
rs10821098	1.00[CEU][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs10992662	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10992669	0.80[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10992674	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs10992698	0.95[CEU][hapmap]
rs1106024	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1109495	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1109496	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11999413	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs12341303	1.00[CEU][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs12349094	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1317698	0.96[CEU][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap]
rs13292831	0.96[CEU][hapmap]
rs13293217	0.85[CEU][hapmap];0.83[MEX][hapmap]
rs1962428	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1970621	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2040093	0.92[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2040094	0.92[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2211535	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs2306183	0.96[CEU][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs4524855	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4743911	0.92[CEU][hapmap]
rs4744185	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4744186	0.81[AMR][1000 genomes]
rs4744192	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4744195	1.00[CEU][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs4744201	1.00[CEU][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs4744206	0.96[CEU][hapmap]
rs4744212	0.96[CEU][hapmap]
rs56039014	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62571716	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7846729	0.85[CEU][hapmap];0.80[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7856802	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7857039	0.91[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7857937	0.92[CEU][hapmap];0.83[CHB][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7868971	1.00[CEU][hapmap];0.84[EUR][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	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	nsv824983	chr9:95902154-95978408	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	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
6	nsv614880	chr9:95930572-95978265	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95950800-95967400	Enhancers	Fetal Heart	heart
2	chr9:95955800-95985600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr9:95956800-95965000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr9:95957000-95963800	Weak transcription	Fetal Kidney	kidney
5	chr9:95957000-95973400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr9:95957200-95963200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr9:95957200-95963400	Weak transcription	Stomach Mucosa	stomach
8	chr9:95957400-95963200	Weak transcription	Fetal Lung	lung
9	chr9:95958000-95963400	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr9:95958200-95963400	Weak transcription	Esophagus	oesophagus
11	chr9:95958200-95966200	Enhancers	Placenta	Placenta
12	chr9:95958200-95972800	Enhancers	Left Ventricle	heart
13	chr9:95958200-95975600	Enhancers	Pancreas	Pancrea
14	chr9:95959000-95967200	Weak transcription	Small Intestine	intestine
15	chr9:95959200-95970200	Weak transcription	Lung	lung
16	chr9:95959400-95963600	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr9:95960200-95964800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr9:95960400-95971400	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr9:95960600-95975800	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr9:95960800-95963600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr9:95961000-95963000	Strong transcription	Fetal Intestine Small	intestine
22	chr9:95961000-95963200	Weak transcription	Fetal Thymus	thymus
23	chr9:95961000-95963400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:95961200-95963400	Weak transcription	K562	blood
25	chr9:95961600-95963200	Weak transcription	Duodenum Mucosa	Duodenum
26	chr9:95961600-95963400	Weak transcription	Gastric	stomach
27	chr9:95961600-95963400	Weak transcription	A549	lung
28	chr9:95961600-95963800	Weak transcription	Right Atrium	heart
29	chr9:95962200-95963400	Enhancers	HepG2	liver
30	chr9:95962200-95963600	Enhancers	Brain Hippocampus Middle	brain
31	chr9:95962200-95970600	Enhancers	Fetal Brain Male	brain
32	chr9:95962200-95973400	Enhancers	Right Ventricle	heart
33	chr9:95962400-95964200	Enhancers	Brain Cingulate Gyrus	brain
34	chr9:95962400-95964400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr9:95962400-95969600	Enhancers	Brain Anterior Caudate	brain
36	chr9:95962600-95963400	Weak transcription	Psoas Muscle	Psoas
37	chr9:95962600-95963600	Weak transcription	Fetal Brain Female	brain
38	chr9:95962600-95963600	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr9:95962600-95964200	Enhancers	Colonic Mucosa	Colon
40	chr9:95962600-95964200	Enhancers	Rectal Mucosa Donor 29	rectum
41	chr9:95962600-95970200	Enhancers	Brain Angular Gyrus	brain
42	chr9:95962800-95963000	Enhancers	H1 Cell Line	embryonic stem cell
43	chr9:95962800-95963000	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr9:95962800-95963000	Flanking Active TSS	Stomach Smooth Muscle	stomach
45	chr9:95962800-95963200	Enhancers	Spleen	Spleen
46	chr9:95962800-95963600	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr9:95962800-95964200	Enhancers	Rectal Smooth Muscle	rectum
48	chr9:95962800-95964400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
49	chr9:95962800-95964600	Enhancers	Brain Germinal Matrix	brain
50	chr9:95962800-95965200	Enhancers	Sigmoid Colon	Sigmoid Colon

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