Variant report

Variant	rs61922044
Chromosome Location	chr12:12490914-12490915
allele	A/G
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	GATA3	chr12:12490711-12491540	SH-SY5Y	brain:	n/a	chr12:12491123-12491134
2	MYC	chr12:12490896-12490965	MCF10A-Er-Src	breast:	n/a	n/a
3	GATA2	chr12:12490748-12491489	SH-SY5Y	brain:	n/a	chr12:12491123-12491134
4	GATA3	chr12:12490568-12491324	SK-N-SH	brain:	n/a	chr12:12491123-12491134
5	E2F4	chr12:12490872-12490924	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr12:12490638-12492149	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:12489787..12492519-chr12:12503031..12504558,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000243141	TF binding region
ENSG00000111261	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs17303178	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17375328	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2160588	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28372890	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3741798	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3825259	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55865572	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55892345	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56829405	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57725255	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61922023	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61922024	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61922025	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61922026	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61922027	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61922028	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61922045	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61922046	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61922047	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61922049	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61922052	1.00[ASN][1000 genomes]
rs61922054	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61922057	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73277486	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73277491	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73279305	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7980482	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv898807	chr12:12448948-12502001	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv898808	chr12:12463407-12549503	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv898809	chr12:12488067-12509314	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12473200-12501600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr12:12473600-12493200	Weak transcription	Fetal Brain Female	brain
3	chr12:12473600-12502000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr12:12473800-12491800	Weak transcription	Left Ventricle	heart
5	chr12:12473800-12502400	Weak transcription	NHLF	lung
6	chr12:12477200-12491800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr12:12480400-12502400	Weak transcription	Right Ventricle	heart
8	chr12:12481200-12491000	Weak transcription	Hela-S3	cervix
9	chr12:12481200-12495400	Weak transcription	Colon Smooth Muscle	Colon
10	chr12:12481200-12502200	Weak transcription	Fetal Heart	heart
11	chr12:12481800-12502400	Weak transcription	Psoas Muscle	Psoas
12	chr12:12482400-12502200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr12:12483600-12502800	Weak transcription	Spleen	Spleen
14	chr12:12484800-12491800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr12:12485400-12500200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr12:12485400-12502400	Weak transcription	Esophagus	oesophagus
17	chr12:12485400-12502800	Weak transcription	Gastric	stomach
18	chr12:12485400-12502800	Weak transcription	Small Intestine	intestine
19	chr12:12486800-12491400	Weak transcription	Primary T cells from cord blood	blood
20	chr12:12486800-12491800	Weak transcription	Brain Angular Gyrus	brain
21	chr12:12487000-12491000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr12:12487200-12491400	Weak transcription	Aorta	Aorta
23	chr12:12487200-12491800	Weak transcription	Ovary	ovary
24	chr12:12487200-12502600	Weak transcription	Fetal Muscle Trunk	muscle
25	chr12:12487400-12491000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr12:12487400-12502200	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr12:12487400-12502200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr12:12487600-12502200	Weak transcription	Colonic Mucosa	Colon
29	chr12:12487800-12491000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr12:12487800-12491200	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr12:12487800-12491200	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr12:12487800-12492800	Weak transcription	Brain Anterior Caudate	brain
33	chr12:12487800-12492800	Weak transcription	Duodenum Mucosa	Duodenum
34	chr12:12488000-12491000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr12:12488000-12491000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr12:12488000-12491600	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr12:12488000-12491600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr12:12488000-12493000	Weak transcription	Brain Substantia Nigra	brain
39	chr12:12488000-12493200	Weak transcription	Adipose Nuclei	Adipose
40	chr12:12488000-12493800	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr12:12488000-12494000	Weak transcription	Brain Hippocampus Middle	brain
42	chr12:12488000-12495000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr12:12488000-12495800	Weak transcription	Brain Cingulate Gyrus	brain
44	chr12:12488000-12495800	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr12:12488000-12502000	Weak transcription	Rectal Smooth Muscle	rectum
46	chr12:12488200-12491000	Weak transcription	A549	lung
47	chr12:12488200-12491200	Weak transcription	Osteobl	bone
48	chr12:12488200-12491800	Weak transcription	Lung	lung
49	chr12:12488200-12495800	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr12:12489200-12497600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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