Variant report

Variant	rs1468878
Chromosome Location	chr12:12393911-12393912
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	chr12:12393044..12397840-chr12:12419223..12421821,5	MCF-7	breast:
2	chr12:12390182..12397827-chr12:12417123..12421502,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000070018	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10431232	0.88[EUR][1000 genomes]
rs10431303	0.88[EUR][1000 genomes]
rs10743981	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1074992	0.88[EUR][1000 genomes]
rs1074993	0.88[EUR][1000 genomes]
rs10772544	0.85[EUR][1000 genomes]
rs10845498	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10845504	0.88[EUR][1000 genomes]
rs10845505	0.82[EUR][1000 genomes]
rs11054701	0.80[EUR][1000 genomes]
rs11054752	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1181333	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1548958	0.88[EUR][1000 genomes]
rs16907786	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16907810	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2075241	0.80[EUR][1000 genomes]
rs2160521	0.80[EUR][1000 genomes]
rs2160589	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2300231	0.81[AFR][1000 genomes]
rs2417090	0.85[EUR][1000 genomes]
rs4265667	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4494380	0.85[EUR][1000 genomes]
rs4619236	0.88[EUR][1000 genomes]
rs4763789	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61130413	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7134001	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7136380	0.83[EUR][1000 genomes]
rs7295656	0.88[EUR][1000 genomes]
rs7310538	0.86[EUR][1000 genomes]
rs7311987	0.85[EUR][1000 genomes]
rs7313285	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7968660	0.87[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:71 , 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	chr12:12379200-12396800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:12383000-12394200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr12:12384800-12417200	Weak transcription	K562	blood
6	chr12:12385000-12394600	Weak transcription	Brain Hippocampus Middle	brain
7	chr12:12385000-12396600	Weak transcription	Left Ventricle	heart
8	chr12:12385000-12396800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr12:12385000-12404000	Weak transcription	Lung	lung
10	chr12:12385000-12417800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr12:12385200-12409200	Weak transcription	Pancreas	Pancrea
12	chr12:12386600-12396800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr12:12389600-12396400	Weak transcription	Fetal Stomach	stomach
14	chr12:12390000-12416600	Weak transcription	Psoas Muscle	Psoas
15	chr12:12390200-12396400	Weak transcription	Fetal Intestine Small	intestine
16	chr12:12390200-12397400	Weak transcription	Small Intestine	intestine
17	chr12:12390400-12398800	Weak transcription	Fetal Muscle Leg	muscle
18	chr12:12390400-12400400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr12:12390600-12396800	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr12:12390800-12417800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr12:12391200-12395200	Weak transcription	Fetal Heart	heart
22	chr12:12391200-12399600	Weak transcription	HSMM	muscle
23	chr12:12391600-12395600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr12:12392200-12396600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr12:12392200-12403000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr12:12392400-12396600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr12:12392400-12396800	Weak transcription	Primary T cells from cord blood	blood
28	chr12:12392400-12397400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr12:12392400-12407800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr12:12392600-12408200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr12:12392800-12394600	Weak transcription	Brain Substantia Nigra	brain
32	chr12:12392800-12394800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr12:12392800-12399800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr12:12393200-12405000	Weak transcription	HUVEC	blood vessel
35	chr12:12393400-12399400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr12:12393600-12394000	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr12:12393600-12394000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
38	chr12:12393600-12394000	Enhancers	Ovary	ovary
39	chr12:12393600-12394000	Flanking Active TSS	HepG2	liver
40	chr12:12393600-12394200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr12:12393600-12394200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr12:12393600-12394200	Active TSS	Pancreatic Islets	Pancreatic Islet
43	chr12:12393600-12394200	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr12:12393600-12394200	Enhancers	Stomach Mucosa	stomach
45	chr12:12393600-12394200	Enhancers	NHLF	lung
46	chr12:12393600-12394400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr12:12393600-12394600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr12:12393600-12394600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr12:12393600-12394600	Active TSS	Fetal Brain Female	brain
50	chr12:12393600-12394800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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