Variant report

Variant	rs13287304
Chromosome Location	chr9:95798871-95798872
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:95797721..95799808-chr9:95800868..95803137,2	MCF-7	breast:
2	chr9:95797648..95801708-chr9:95856413..95859083,5	MCF-7	breast:
3	chr9:95780776..95784501-chr9:95797559..95801380,3	MCF-7	breast:
4	chr9:95797004..95799082-chr9:95868699..95871377,2	K562	blood:
5	chr9:95797817..95800116-chr9:95854194..95855844,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165233	Chromatin interaction
ENSG00000223446	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10115178	1.00[ASN][1000 genomes]
rs10115813	1.00[ASN][1000 genomes]
rs10117910	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10821056	0.82[ASW][hapmap];0.88[CEU][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10821057	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10992583	0.82[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10992585	0.88[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10992590	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10992593	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10992602	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1127857	1.00[CHB][hapmap]
rs12005054	1.00[CHB][hapmap]
rs13284731	1.00[CHB][hapmap]
rs13285107	1.00[CHB][hapmap]
rs13294417	1.00[CHB][hapmap]
rs13298119	1.00[CHB][hapmap]
rs13299270	1.00[CHB][hapmap]
rs28715500	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34002351	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34274030	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34337651	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs36044170	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56226047	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7024692	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7048701	1.00[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap]
rs7852416	1.00[CHB][hapmap];0.81[CHD][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7854887	0.82[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs7855476	1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.85[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	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	nsv1054767	chr9:95738134-95875977	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1035230	chr9:95770249-95934982	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv893575	chr9:95781040-95854013	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv521136	chr9:95782667-95798871	Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region	6 gene(s)	inside rSNPs	n/a
6	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13287304	ZNF484	cis	cerebellum	SCAN
rs13287304	NCBP1	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95776600-95799200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:95776600-95799400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr9:95783600-95799000	Weak transcription	Esophagus	oesophagus
4	chr9:95791000-95800400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr9:95791200-95799800	Strong transcription	Thymus	Thymus
6	chr9:95791400-95799800	Genic enhancers	Primary T cells fromperipheralblood	blood
7	chr9:95791400-95800000	Genic enhancers	Primary monocytes fromperipheralblood	blood
8	chr9:95791400-95800000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr9:95791800-95799800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
10	chr9:95792000-95799200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr9:95792000-95800000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr9:95792800-95799000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr9:95794400-95800000	Weak transcription	Liver	Liver
14	chr9:95795000-95799800	Genic enhancers	Primary neutrophils fromperipheralblood	blood
15	chr9:95795200-95799000	Strong transcription	Lung	lung
16	chr9:95795200-95800400	Weak transcription	Duodenum Mucosa	Duodenum
17	chr9:95795200-95801400	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr9:95796000-95799000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr9:95796400-95799000	Strong transcription	Fetal Thymus	thymus
20	chr9:95796400-95799400	Genic enhancers	Monocytes-CD14+_RO01746	blood
21	chr9:95796600-95799400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr9:95796600-95799400	Strong transcription	Spleen	Spleen
23	chr9:95796600-95799400	Weak transcription	GM12878-XiMat	blood
24	chr9:95796600-95800400	Weak transcription	Fetal Intestine Large	intestine
25	chr9:95796800-95799400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr9:95797000-95799200	Strong transcription	Fetal Intestine Small	intestine
27	chr9:95797200-95799200	Weak transcription	Adipose Nuclei	Adipose
28	chr9:95797400-95800800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr9:95797600-95799000	Strong transcription	Fetal Stomach	stomach
30	chr9:95797600-95799400	Weak transcription	Right Ventricle	heart
31	chr9:95798000-95799000	Weak transcription	Fetal Muscle Leg	muscle
32	chr9:95798000-95799200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr9:95798000-95802400	Weak transcription	Gastric	stomach
34	chr9:95798200-95799000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr9:95798200-95799600	Genic enhancers	Primary T cells from cord blood	blood
36	chr9:95798200-95800600	Weak transcription	Fetal Brain Female	brain
37	chr9:95798200-95800800	Enhancers	Primary hematopoietic stem cells	blood
38	chr9:95798400-95799600	Weak transcription	Primary B cells from cord blood	blood
39	chr9:95798400-95799600	Weak transcription	K562	blood
40	chr9:95798400-95800200	Weak transcription	Brain Germinal Matrix	brain
41	chr9:95798400-95801400	Enhancers	Placenta	Placenta
42	chr9:95798400-95801800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr9:95798600-95800400	Enhancers	Fetal Muscle Trunk	muscle
44	chr9:95798600-95800600	Weak transcription	Dnd41	blood
45	chr9:95798800-95799000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr9:95798800-95799200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr9:95798800-95799200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr9:95798800-95799800	Genic enhancers	Primary B cells from peripheral blood	blood
49	chr9:95798800-95800200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr9:95798800-95804200	Enhancers	Primary T helper cells PMA-I stimulated	--

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