Variant report

Variant	rs10992599
Chromosome Location	chr9:95800202-95800203
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:95798879..95801785-chr9:95811313..95813235,2	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:

Variant related genes	Relation type
ENSG00000165233	Chromatin interaction
ENSG00000223446	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10992556	0.85[CEU][hapmap]
rs10992557	1.00[CEU][hapmap]
rs10992569	0.90[EUR][1000 genomes]
rs10992576	0.86[EUR][1000 genomes]
rs10992577	0.96[EUR][1000 genomes]
rs10992578	0.96[EUR][1000 genomes]
rs10992579	0.96[EUR][1000 genomes]
rs10992580	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10992584	0.85[CEU][hapmap];1.00[EUR][1000 genomes]
rs10992586	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10992587	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10992588	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10992601	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10992605	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10992607	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12377562	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs12380201	0.90[EUR][1000 genomes]
rs12380291	0.85[CEU][hapmap];1.00[EUR][1000 genomes]
rs12380789	0.90[EUR][1000 genomes]
rs41273404	0.90[EUR][1000 genomes]
rs55654224	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7043408	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs72741052	0.90[EUR][1000 genomes]
rs72741055	0.96[EUR][1000 genomes]
rs72741057	0.96[EUR][1000 genomes]
rs72741060	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72741063	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9696630	0.85[CEU][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95791000-95800400	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr9:95795200-95800400	Weak transcription	Duodenum Mucosa	Duodenum
3	chr9:95795200-95801400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr9:95796600-95800400	Weak transcription	Fetal Intestine Large	intestine
5	chr9:95797400-95800800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr9:95798000-95802400	Weak transcription	Gastric	stomach
7	chr9:95798200-95800600	Weak transcription	Fetal Brain Female	brain
8	chr9:95798200-95800800	Enhancers	Primary hematopoietic stem cells	blood
9	chr9:95798400-95801400	Enhancers	Placenta	Placenta
10	chr9:95798400-95801800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr9:95798600-95800400	Enhancers	Fetal Muscle Trunk	muscle
12	chr9:95798600-95800600	Weak transcription	Dnd41	blood
13	chr9:95798800-95804200	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr9:95799000-95800800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr9:95799200-95800400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr9:95799200-95800600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr9:95799200-95800600	Enhancers	Adipose Nuclei	Adipose
18	chr9:95799200-95800800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr9:95799200-95800800	Enhancers	Fetal Thymus	thymus
20	chr9:95799200-95801000	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr9:95799400-95800400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr9:95799400-95800400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr9:95799400-95800600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr9:95799400-95800800	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr9:95799400-95801000	Enhancers	GM12878-XiMat	blood
26	chr9:95799600-95800800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
27	chr9:95799600-95801000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr9:95799600-95801600	Enhancers	Primary B cells from cord blood	blood
29	chr9:95799600-95802000	Enhancers	Primary T cells from cord blood	blood
30	chr9:95799800-95800800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr9:95799800-95800800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr9:95799800-95801000	Enhancers	Primary B cells from peripheral blood	blood
33	chr9:95799800-95803000	Weak transcription	Spleen	Spleen
34	chr9:95799800-95804200	Enhancers	Primary T cells fromperipheralblood	blood
35	chr9:95799800-95805200	Weak transcription	K562	blood
36	chr9:95799800-95806600	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr9:95799800-95815600	Weak transcription	Thymus	Thymus
38	chr9:95800000-95800400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr9:95800000-95800600	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr9:95800000-95800800	Enhancers	Liver	Liver
41	chr9:95800000-95801800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr9:95800000-95806600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr9:95800000-95809800	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr9:95800200-95800400	Enhancers	Brain Germinal Matrix	brain
45	chr9:95800200-95800400	Enhancers	Lung	lung
46	chr9:95800200-95800600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr9:95800200-95800800	Enhancers	iPS-15b Cell Line	embryonic stem cell
48	chr9:95800200-95800800	Enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr9:95800200-95800800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
50	chr9:95800200-95800800	Enhancers	Fetal Muscle Leg	muscle

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