Variant report

Variant	rs17009899
Chromosome Location	chr12:83114874-83114875
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	chr12:83104932..83106856-chr12:83113427..83114996,2	K562	blood:
2	chr12:83103199..83104985-chr12:83114072..83116122,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10506878	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10862497	0.88[EUR][1000 genomes]
rs11115342	0.80[EUR][1000 genomes]
rs11115348	0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs11115353	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11115355	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[EUR][1000 genomes]
rs11609532	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11609597	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11610988	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11611431	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11613168	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11614435	1.00[ASW][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11615763	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11615765	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12305736	0.80[EUR][1000 genomes]
rs12307168	0.80[EUR][1000 genomes]
rs12423043	0.80[EUR][1000 genomes]
rs12426166	0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs13377925	0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs17009851	0.80[EUR][1000 genomes]
rs17009854	1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17009856	0.80[EUR][1000 genomes]
rs17009879	0.87[YRI][hapmap]
rs17009882	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17009885	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17009891	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17009893	1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1922576	0.80[EUR][1000 genomes]
rs1922579	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4620789	0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs4882428	0.81[EUR][1000 genomes]
rs55657485	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56298822	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56396658	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61485473	0.80[EUR][1000 genomes]
rs6539683	0.87[EUR][1000 genomes]
rs7134747	0.86[EUR][1000 genomes]
rs7134766	0.87[EUR][1000 genomes]
rs7135486	0.91[EUR][1000 genomes]
rs72615654	0.83[EUR][1000 genomes]
rs7294890	0.83[EUR][1000 genomes]
rs7303469	0.90[EUR][1000 genomes]
rs7313778	0.91[EUR][1000 genomes]
rs74106267	0.80[EUR][1000 genomes]
rs7961953	0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs7975647	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053093	chr12:82645292-83287809	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv541551	chr12:82645292-83287809	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv899348	chr12:82744187-83169297	Enhancers Strong transcription Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv427917	chr12:82917031-83279712	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv521849	chr12:83013783-83991479	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv469490	chr12:83089431-83507269	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv559542	chr12:83089431-83507269	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	esv2758315	chr12:83101045-83357621	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	esv2759911	chr12:83101045-83357621	Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	esv2755991	chr12:83105631-83248605	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv469491	chr12:83108395-83203742	Enhancers Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv559543	chr12:83108395-83203742	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:83086600-83122200	Weak transcription	Fetal Muscle Trunk	muscle
2	chr12:83093200-83122400	Weak transcription	Gastric	stomach
3	chr12:83098000-83121200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr12:83099200-83122400	Weak transcription	Esophagus	oesophagus
5	chr12:83102400-83138800	Weak transcription	Fetal Kidney	kidney
6	chr12:83102600-83122200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr12:83102600-83122400	Weak transcription	Lung	lung
8	chr12:83102600-83140600	Weak transcription	Pancreas	Pancrea
9	chr12:83102800-83122400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:83102800-83134000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr12:83103000-83115400	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr12:83103200-83124000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr12:83105800-83117400	Weak transcription	Colon Smooth Muscle	Colon
14	chr12:83106000-83122200	Weak transcription	Fetal Intestine Small	intestine
15	chr12:83106800-83115600	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr12:83106800-83133800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr12:83107000-83117000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr12:83107000-83127800	Weak transcription	Fetal Muscle Leg	muscle
19	chr12:83107400-83121200	Weak transcription	Fetal Stomach	stomach
20	chr12:83109200-83115800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr12:83109200-83120400	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr12:83109600-83120600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:83111800-83115400	Weak transcription	Fetal Heart	heart
24	chr12:83112600-83124200	Weak transcription	Fetal Lung	lung
25	chr12:83113000-83138600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr12:83113200-83124600	Weak transcription	Fetal Brain Male	brain
27	chr12:83113600-83117600	Weak transcription	Left Ventricle	heart
28	chr12:83114000-83116000	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr12:83114400-83115000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr12:83114600-83115000	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr12:83114600-83115600	Enhancers	Brain Hippocampus Middle	brain
32	chr12:83114800-83115200	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr12:83114800-83115200	Enhancers	Brain Cingulate Gyrus	brain
34	chr12:83114800-83115800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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