Variant report

Variant	rs74061140
Chromosome Location	chr12:12374871-12374872
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	IKZF1	chr12:12374543-12374927	GM12878	blood:	n/a	n/a
2	FOXA1	chr12:12374405-12374885	A549	lung:	n/a	n/a
3	TCF12	chr12:12374160-12374906	A549	lung:	n/a	n/a
4	NR3C1	chr12:12374377-12374896	A549	lung:	n/a	chr12:12374621-12374637 chr12:12374622-12374636 chr12:12374622-12374636 chr12:12374618-12374639 chr12:12374621-12374637 chr12:12374620-12374637 chr12:12374622-12374636 chr12:12374841-12374848 chr12:12374619-12374640 chr12:12374620-12374638 chr12:12374621-12374637 chr12:12374621-12374637

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:12373050..12374895-chr12:12377294..12378845,2	MCF-7	breast:

Variant related genes	Relation type
RNU6-545P	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11054762	1.00[ASN][1000 genomes]
rs11054765	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12313063	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12321230	1.00[ASN][1000 genomes]
rs57125171	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs58389257	1.00[EUR][1000 genomes]
rs73275029	1.00[ASN][1000 genomes]
rs73275034	1.00[ASN][1000 genomes]
rs73275042	1.00[ASN][1000 genomes]
rs73293337	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74061124	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74061127	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74061139	0.85[AFR][1000 genomes]
rs74061143	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74061144	0.85[AFR][1000 genomes]
rs74061150	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74061155	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74061157	1.00[ASN][1000 genomes]
rs74061158	1.00[EUR][1000 genomes];1.00[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	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv529005	chr12:12254756-12412795	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	esv3427115	chr12:12262415-12432411	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
4	nsv898806	chr12:12264471-12453808	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1050715	chr12:12293072-12383820	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv832332	chr12:12344027-12484966	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12336200-12381000	Weak transcription	Pancreas	Pancrea
2	chr12:12344200-12377000	Weak transcription	NHDF-Ad	bronchial
3	chr12:12367800-12375400	Enhancers	HepG2	liver
4	chr12:12368200-12376200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr12:12368200-12376200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr12:12368200-12379000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr12:12368200-12381400	Weak transcription	Gastric	stomach
8	chr12:12368200-12384200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:12368400-12417200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr12:12368600-12381000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr12:12368600-12381400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr12:12370600-12380800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr12:12370600-12381000	Weak transcription	Left Ventricle	heart
14	chr12:12370800-12379000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:12370800-12380800	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr12:12370800-12392200	Weak transcription	Brain Substantia Nigra	brain
17	chr12:12371200-12376200	Weak transcription	Brain Anterior Caudate	brain
18	chr12:12371600-12375200	Enhancers	Liver	Liver
19	chr12:12371800-12378200	Weak transcription	Fetal Muscle Leg	muscle
20	chr12:12372000-12376200	Weak transcription	GM12878-XiMat	blood
21	chr12:12372200-12376800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr12:12373000-12380800	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr12:12373000-12381200	Weak transcription	Lung	lung
24	chr12:12373800-12375000	Enhancers	Colon Smooth Muscle	Colon
25	chr12:12373800-12375000	Flanking Active TSS	A549	lung
26	chr12:12373800-12375200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr12:12374000-12375000	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr12:12374000-12375200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr12:12374000-12377800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr12:12374200-12375000	Enhancers	Fetal Intestine Large	intestine
31	chr12:12374200-12376600	Weak transcription	K562	blood
32	chr12:12374400-12375000	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr12:12374400-12376000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr12:12374600-12375000	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr12:12374600-12375000	Enhancers	Brain Cingulate Gyrus	brain
36	chr12:12374600-12375000	Enhancers	Duodenum Mucosa	Duodenum
37	chr12:12374600-12375000	Weak transcription	Fetal Kidney	kidney
38	chr12:12374600-12375000	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr12:12374600-12375000	Enhancers	HSMM	muscle
40	chr12:12374600-12377000	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr12:12374600-12381000	Weak transcription	Brain Hippocampus Middle	brain
42	chr12:12374600-12381400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr12:12374800-12375000	Weak transcription	Ovary	ovary
44	chr12:12374800-12380600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr12:12374800-12380600	Weak transcription	Brain Angular Gyrus	brain
46	chr12:12374800-12380800	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr12:12374800-12383200	Weak transcription	Skeletal Muscle Female	skeletal muscle

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