Variant report

Variant	rs74061145
Chromosome Location	chr12:12400652-12400653
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	GATA3	chr12:12400385-12400963	SK-N-SH	brain:	n/a	chr12:12400632-12400639
2	EP300	chr12:12400492-12400735	SK-N-SH_RA	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:12399729..12401467-chr12:12407423..12408972,2	K562	blood:
2	chr12:12399860..12402436-chr12:12417674..12420343,2	K562	blood:
3	chr12:12395975..12398553-chr12:12399397..12402094,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MANSC1-1	chr12:12399611-12401006	l_612_NR_024061

Variant related genes	Relation type
ENSG00000270857	TF binding region
LRP6	TF binding region
ENSG00000070018	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10082834	0.85[EUR][1000 genomes]
rs10083170	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10845497	0.92[EUR][1000 genomes]
rs10845499	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10845500	0.90[EUR][1000 genomes]
rs11054720	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054729	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054732	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054746	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11829211	0.83[EUR][1000 genomes]
rs12297598	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12304957	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12307111	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12311922	0.92[EUR][1000 genomes]
rs12319942	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12425185	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12427198	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28448423	0.92[EUR][1000 genomes]
rs56087862	0.80[AMR][1000 genomes]
rs56998126	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57055264	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58682800	0.87[EUR][1000 genomes]
rs7308022	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311064	0.85[EUR][1000 genomes]
rs74061123	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7957531	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7960716	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973583	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973718	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7978064	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7979919	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12368400-12417200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr12:12377800-12407200	Weak transcription	NH-A	brain
3	chr12:12384800-12417200	Weak transcription	K562	blood
4	chr12:12385000-12404000	Weak transcription	Lung	lung
5	chr12:12385000-12417800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr12:12385200-12409200	Weak transcription	Pancreas	Pancrea
7	chr12:12390000-12416600	Weak transcription	Psoas Muscle	Psoas
8	chr12:12390800-12417800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr12:12392200-12403000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr12:12392400-12407800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr12:12392600-12408200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr12:12393200-12405000	Weak transcription	HUVEC	blood vessel
13	chr12:12394200-12407200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr12:12394200-12407200	Weak transcription	Osteobl	bone
15	chr12:12394200-12416800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr12:12394200-12417400	Weak transcription	Fetal Kidney	kidney
17	chr12:12394400-12401000	Weak transcription	Colon Smooth Muscle	Colon
18	chr12:12394600-12407600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr12:12394800-12405800	Weak transcription	HMEC	breast
20	chr12:12394800-12407600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr12:12394800-12417400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr12:12395200-12407200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr12:12395600-12409200	Weak transcription	Ovary	ovary
24	chr12:12395600-12417400	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr12:12395800-12406600	Weak transcription	Brain Germinal Matrix	brain
26	chr12:12396000-12407400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr12:12397000-12403600	Weak transcription	Fetal Intestine Small	intestine
28	chr12:12397000-12408400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr12:12397400-12403200	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr12:12397400-12409600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr12:12397600-12400800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr12:12397600-12401800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr12:12397600-12402200	Weak transcription	Fetal Thymus	thymus
34	chr12:12397600-12404600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr12:12397600-12404600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr12:12397600-12404800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr12:12397600-12404800	Weak transcription	Left Ventricle	heart
38	chr12:12397600-12406200	Weak transcription	Primary T cells from cord blood	blood
39	chr12:12397600-12407600	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr12:12397600-12409400	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr12:12397600-12416600	Weak transcription	Fetal Stomach	stomach
42	chr12:12397800-12405200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr12:12397800-12416800	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr12:12397800-12417200	Weak transcription	Brain Anterior Caudate	brain
45	chr12:12398000-12401000	Weak transcription	Brain Substantia Nigra	brain
46	chr12:12398200-12404400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr12:12398200-12404600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr12:12398200-12407400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr12:12398400-12406800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr12:12398800-12400800	Weak transcription	Brain Cingulate Gyrus	brain

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