Variant report

Variant	rs17009868
Chromosome Location	chr12:83102683-83102684
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:83078166..83081005-chr12:83099084..83103387,3	MCF-7	breast:
2	chr12:83101540..83104228-chr12:83107720..83109388,2	MCF-7	breast:
3	chr12:83097820..83099718-chr12:83101247..83102887,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000179104	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12313503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12425493	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12578600	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13378007	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17009829	0.84[AMR][1000 genomes]
rs17009859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17009863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1882582	0.92[MEX][hapmap];0.91[AMR][1000 genomes]
rs1922578	0.84[AMR][1000 genomes]
rs4882521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4882522	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57227638	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57715118	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60454381	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6539680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7294774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7303441	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7306509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7311617	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311886	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7313780	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7315791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74106266	0.91[AMR][1000 genomes]
rs74106270	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7979455	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv559541	chr12:82715210-83108395	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats 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	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
5	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
6	nsv899349	chr12:82931646-83114286	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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
11	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17009868	TCFL5	trans	brain	seeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:83086600-83122200	Weak transcription	Fetal Muscle Trunk	muscle
2	chr12:83087200-83105600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr12:83087400-83106400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr12:83093200-83122400	Weak transcription	Gastric	stomach
5	chr12:83095400-83106600	Weak transcription	Fetal Intestine Large	intestine
6	chr12:83096000-83105800	Weak transcription	Fetal Intestine Small	intestine
7	chr12:83098000-83121200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr12:83098800-83106800	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr12:83099200-83122400	Weak transcription	Esophagus	oesophagus
10	chr12:83099400-83103800	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr12:83100400-83103200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr12:83100600-83102800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:83100600-83103000	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr12:83100800-83102800	Enhancers	Fetal Heart	heart
15	chr12:83101000-83102800	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr12:83101000-83104800	Enhancers	Rectal Smooth Muscle	rectum
17	chr12:83101200-83102800	Enhancers	Fetal Muscle Leg	muscle
18	chr12:83101200-83102800	Enhancers	Placenta Amnion	Placenta Amnion
19	chr12:83101200-83103000	Enhancers	Fetal Stomach	stomach
20	chr12:83101400-83102800	Enhancers	H9 Cell Line	embryonic stem cell
21	chr12:83101400-83102800	Active TSS	Fetal Brain Male	brain
22	chr12:83101400-83102800	Enhancers	Ovary	ovary
23	chr12:83101400-83102800	Enhancers	GM12878-XiMat	blood
24	chr12:83101600-83102800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr12:83101600-83102800	Enhancers	Fetal Lung	lung
26	chr12:83101600-83103200	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr12:83101800-83102800	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr12:83101800-83103400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr12:83102000-83102800	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr12:83102000-83102800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr12:83102000-83102800	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr12:83102000-83102800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr12:83102000-83102800	Flanking Active TSS	Stomach Smooth Muscle	stomach
34	chr12:83102000-83103000	Enhancers	H1 Cell Line	embryonic stem cell
35	chr12:83102200-83102800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr12:83102200-83102800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr12:83102200-83103000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr12:83102200-83103000	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr12:83102200-83103000	Flanking Active TSS	Colon Smooth Muscle	Colon
40	chr12:83102200-83103800	Enhancers	iPS-20b Cell Line	embryonic stem cell
41	chr12:83102400-83102800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr12:83102400-83102800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
43	chr12:83102400-83103200	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr12:83102400-83104000	Enhancers	Brain Cingulate Gyrus	brain
45	chr12:83102400-83138800	Weak transcription	Fetal Kidney	kidney
46	chr12:83102600-83102800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr12:83102600-83102800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr12:83102600-83103000	Enhancers	Brain Anterior Caudate	brain
49	chr12:83102600-83103200	Enhancers	Brain Hippocampus Middle	brain
50	chr12:83102600-83103400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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