Variant report

Variant	rs17085969
Chromosome Location	chr9:85640254-85640255
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:85639962..85642383-chr9:85676276..85678231,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C9orf103-7	chr9:85634340-85642318	predAs_engstrom06_AI205792_1

Variant related genes	Relation type
ENSG00000165105	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs17085959	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17085961	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17085962	0.93[YRI][hapmap];0.89[AFR][1000 genomes]
rs17085963	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17085973	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17085980	0.92[YRI][hapmap]
rs17085982	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17085986	0.86[YRI][hapmap];0.98[AFR][1000 genomes]
rs17085988	0.87[YRI][hapmap];0.98[AFR][1000 genomes]
rs56751483	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58019119	1.00[AMR][1000 genomes]
rs58323931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58387961	0.98[AFR][1000 genomes]
rs59113785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59707822	0.98[AFR][1000 genomes]
rs7030604	0.85[YRI][hapmap]
rs7043044	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7043189	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7043478	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73467584	1.00[AMR][1000 genomes]
rs73467586	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73467588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73467594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73467600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73469405	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73469407	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73469408	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73469410	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73469413	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73469415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73469417	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73469420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73469421	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73469424	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73469427	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73469429	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73469430	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73469432	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73469434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73469435	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73469438	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73469447	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73469468	0.98[AFR][1000 genomes]
rs73469475	0.98[AFR][1000 genomes]
rs73469481	0.98[AFR][1000 genomes]
rs73469484	0.98[AFR][1000 genomes]
rs73469487	0.98[AFR][1000 genomes]
rs73469492	0.94[AFR][1000 genomes]
rs73469496	0.98[AFR][1000 genomes]
rs73469497	0.98[AFR][1000 genomes]
rs73469499	0.98[AFR][1000 genomes]
rs73471405	0.98[AFR][1000 genomes]
rs73471407	0.98[AFR][1000 genomes]
rs73471410	0.98[AFR][1000 genomes]
rs7470762	0.98[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050771	chr9:85416931-85643417	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv893511	chr9:85495968-85833127	Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription 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:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:85603200-85643800	Weak transcription	Duodenum Mucosa	Duodenum
2	chr9:85610800-85642000	Weak transcription	Fetal Intestine Large	intestine
3	chr9:85613600-85643400	Weak transcription	Colonic Mucosa	Colon
4	chr9:85617200-85645800	Weak transcription	Stomach Mucosa	stomach
5	chr9:85621000-85645400	Weak transcription	Gastric	stomach
6	chr9:85623600-85643200	Weak transcription	Fetal Intestine Small	intestine
7	chr9:85628600-85643400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr9:85630000-85641600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr9:85635600-85641400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr9:85635600-85641800	Weak transcription	Esophagus	oesophagus
11	chr9:85636200-85641400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr9:85636400-85643600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr9:85637400-85641400	Weak transcription	Pancreas	Pancrea
14	chr9:85637400-85643200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr9:85639200-85641200	Weak transcription	A549	lung
16	chr9:85639400-85640800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr9:85639400-85640800	Enhancers	Placenta	Placenta
18	chr9:85639800-85640400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr9:85639800-85640400	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr9:85639800-85640400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr9:85639800-85640400	Enhancers	NHDF-Ad	bronchial
22	chr9:85639800-85645000	Enhancers	HMEC	breast
23	chr9:85640000-85641400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr9:85640000-85641600	Weak transcription	Osteobl	bone
25	chr9:85640000-85641800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr9:85640000-85641800	Weak transcription	NHLF	lung
27	chr9:85640200-85642000	Weak transcription	Placenta Amnion	Placenta Amnion

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