Variant report

Variant	rs10821090
Chromosome Location	chr9:95963863-95963864
allele	C/G
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:95963731..95965841-chr9:96218662..96220646,2	MCF-7	breast:
2	chr9:95961414..95965641-chr9:95984083..95987391,7	MCF-7	breast:
3	chr9:95894082..95896829-chr9:95963549..95967128,4	MCF-7	breast:
4	chr9:95962951..95965584-chr9:95975622..95978516,3	MCF-7	breast:
5	chr9:95957079..95960371-chr9:95962427..95964398,3	K562	blood:
6	chr9:95894379..95898101-chr9:95963413..95967627,3	MCF-7	breast:
7	chr9:95963232..95968490-chr9:95968804..95973983,9	MCF-7	breast:
8	chr9:95944881..95947924-chr9:95961775..95965090,3	MCF-7	breast:
9	chr9:95961633..95964476-chr9:96008257..96009882,2	MCF-7	breast:
10	chr9:95962461..95964580-chr9:96059375..96061154,2	MCF-7	breast:
11	chr9:95958543..95960767-chr9:95962228..95964841,3	MCF-7	breast:
12	chr9:95963712..95965876-chr9:96038705..96040305,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000131669	Chromatin interaction
ENSG00000165238	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10761200	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10821080	0.82[CHB][hapmap]
rs10821084	0.91[JPT][hapmap]
rs10821086	0.81[JPT][hapmap]
rs10821088	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs10821089	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10992669	0.83[JPT][hapmap]
rs10992674	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1106952	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11999413	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12336667	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs1317939	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2040093	0.81[JPT][hapmap]
rs2040094	0.81[JPT][hapmap]
rs2211535	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7857039	0.85[JPT][hapmap]
rs7857187	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7857937	0.81[JPT][hapmap]

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	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
7	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10821090	C9orf102	cis	cerebellum	SCAN

Chromatin state (count:64 , 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	chr9:95957000-95973400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr9:95958200-95966200	Enhancers	Placenta	Placenta
6	chr9:95958200-95972800	Enhancers	Left Ventricle	heart
7	chr9:95958200-95975600	Enhancers	Pancreas	Pancrea
8	chr9:95959000-95967200	Weak transcription	Small Intestine	intestine
9	chr9:95959200-95970200	Weak transcription	Lung	lung
10	chr9:95960200-95964800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr9:95960400-95971400	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr9:95960600-95975800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr9:95962200-95970600	Enhancers	Fetal Brain Male	brain
14	chr9:95962200-95973400	Enhancers	Right Ventricle	heart
15	chr9:95962400-95964200	Enhancers	Brain Cingulate Gyrus	brain
16	chr9:95962400-95964400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr9:95962400-95969600	Enhancers	Brain Anterior Caudate	brain
18	chr9:95962600-95964200	Enhancers	Colonic Mucosa	Colon
19	chr9:95962600-95964200	Enhancers	Rectal Mucosa Donor 29	rectum
20	chr9:95962600-95970200	Enhancers	Brain Angular Gyrus	brain
21	chr9:95962800-95964200	Enhancers	Rectal Smooth Muscle	rectum
22	chr9:95962800-95964400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
23	chr9:95962800-95964600	Enhancers	Brain Germinal Matrix	brain
24	chr9:95962800-95965200	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr9:95962800-95967400	Enhancers	Colon Smooth Muscle	Colon
26	chr9:95962800-95972600	Enhancers	Fetal Muscle Leg	muscle
27	chr9:95962800-95975600	Enhancers	Fetal Intestine Large	intestine
28	chr9:95963200-95964000	Bivalent Enhancer	Fetal Stomach	stomach
29	chr9:95963200-95964200	Enhancers	Duodenum Mucosa	Duodenum
30	chr9:95963200-95964800	Enhancers	Fetal Lung	lung
31	chr9:95963200-95966200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr9:95963200-95970800	Enhancers	Fetal Thymus	thymus
33	chr9:95963200-95971200	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr9:95963400-95964000	Enhancers	Stomach Mucosa	stomach
35	chr9:95963400-95964000	Enhancers	K562	blood
36	chr9:95963400-95964600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr9:95963400-95964600	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr9:95963400-95964600	Flanking Active TSS	Stomach Smooth Muscle	stomach
39	chr9:95963400-95964600	Enhancers	A549	lung
40	chr9:95963400-95964800	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr9:95963400-95964800	Enhancers	Brain Substantia Nigra	brain
42	chr9:95963400-95964800	Enhancers	Esophagus	oesophagus
43	chr9:95963400-95964800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr9:95963400-95965400	Enhancers	Gastric	stomach
45	chr9:95963400-95965800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr9:95963400-95966400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr9:95963400-95967600	Enhancers	Fetal Intestine Small	intestine
48	chr9:95963400-95968400	Flanking Active TSS	HepG2	liver
49	chr9:95963400-95972800	Enhancers	Psoas Muscle	Psoas
50	chr9:95963600-95964000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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