Variant report

Variant	rs12309762
Chromosome Location	chr12:9830698-9830699
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	POLR2A	chr12:9830600-9830728	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:9799376..9803211-chr12:9829355..9833223,4	MCF-7	breast:
2	chr12:9816317..9819269-chr12:9830012..9832319,2	K562	blood:
3	chr12:9824522..9827261-chr12:9829705..9832402,3	MCF-7	breast:

Variant related genes	Relation type
CLEC2D	TF binding region
ENSG00000069493	Chromatin interaction
ENSG00000256594	Chromatin interaction
ENSG00000256442	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1008611	0.83[ASN][1000 genomes]
rs10743821	0.83[ASN][1000 genomes]
rs10743822	0.83[ASN][1000 genomes]
rs10844418	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844424	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10844429	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10844449	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10844457	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10844476	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052303	0.94[ASN][1000 genomes]
rs11052304	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11052305	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052311	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052327	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052342	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052367	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052430	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052431	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052434	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052718	0.83[ASN][1000 genomes]
rs11052785	0.83[ASN][1000 genomes]
rs11519377	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11524523	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12320830	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12578698	0.83[ASN][1000 genomes]
rs12578928	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12582616	0.83[ASN][1000 genomes]
rs12810851	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12815393	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12817365	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12823699	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12825507	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12828602	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12828773	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12831453	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1990533	0.83[ASN][1000 genomes]
rs2114872	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2114873	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2192433	0.83[ASN][1000 genomes]
rs2192434	0.83[ASN][1000 genomes]
rs2192435	0.83[ASN][1000 genomes]
rs2192439	0.89[ASN][1000 genomes]
rs2401396	0.83[ASN][1000 genomes]
rs34201389	0.83[ASN][1000 genomes]
rs35237063	1.00[ASN][1000 genomes]
rs4763264	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4763835	0.83[ASN][1000 genomes]
rs61913428	0.83[ASN][1000 genomes]
rs6488109	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488122	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7310897	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7954062	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7962025	0.81[EUR][1000 genomes]
rs7969074	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7969441	0.85[AFR][1000 genomes]
rs7972035	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7979758	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9630264	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9630265	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9668568	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs982511	0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
2	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12309762	LOC374443	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9802400-9849800	Weak transcription	Pancreas	Pancrea
2	chr12:9807600-9847200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr12:9815200-9840600	Weak transcription	Fetal Brain Male	brain
4	chr12:9815200-9841600	Weak transcription	Fetal Kidney	kidney
5	chr12:9815600-9833800	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr12:9816200-9832600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr12:9816200-9840600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr12:9817200-9837800	Weak transcription	Aorta	Aorta
9	chr12:9818000-9839200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr12:9818000-9839800	Weak transcription	Ovary	ovary
11	chr12:9818000-9840000	Weak transcription	Fetal Intestine Large	intestine
12	chr12:9818000-9849800	Weak transcription	Brain Germinal Matrix	brain
13	chr12:9818200-9840000	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr12:9824400-9832600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr12:9826400-9849000	Weak transcription	Psoas Muscle	Psoas
16	chr12:9826600-9847200	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr12:9826600-9852400	Weak transcription	Colon Smooth Muscle	Colon
18	chr12:9826800-9832200	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr12:9826800-9833400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr12:9826800-9833800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr12:9826800-9837400	Weak transcription	Fetal Muscle Trunk	muscle
22	chr12:9826800-9840000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr12:9826800-9840600	Weak transcription	HSMMtube	muscle
24	chr12:9826800-9841000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr12:9826800-9841400	Weak transcription	Duodenum Mucosa	Duodenum
26	chr12:9826800-9844600	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr12:9826800-9848400	Weak transcription	Colonic Mucosa	Colon
28	chr12:9826800-9849400	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr12:9826800-9849800	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr12:9826800-9854400	Weak transcription	Esophagus	oesophagus
31	chr12:9827000-9832200	Weak transcription	Placenta	Placenta
32	chr12:9827000-9832600	Weak transcription	Fetal Lung	lung
33	chr12:9827000-9837400	Weak transcription	Right Ventricle	heart
34	chr12:9827000-9840800	Weak transcription	Adipose Nuclei	Adipose
35	chr12:9827000-9853200	Weak transcription	Rectal Smooth Muscle	rectum
36	chr12:9827200-9830800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr12:9827200-9832400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr12:9827200-9832400	Weak transcription	Fetal Thymus	thymus
39	chr12:9827200-9832400	Weak transcription	K562	blood
40	chr12:9827200-9832600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr12:9827200-9832600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr12:9827200-9832800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr12:9827200-9834000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr12:9827200-9835000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr12:9827200-9835000	Weak transcription	Fetal Muscle Leg	muscle
46	chr12:9827200-9837600	Weak transcription	Fetal Heart	heart
47	chr12:9827200-9837800	Weak transcription	Fetal Intestine Small	intestine
48	chr12:9827200-9837800	Weak transcription	Fetal Stomach	stomach
49	chr12:9827200-9837800	Weak transcription	Left Ventricle	heart
50	chr12:9827200-9838400	Weak transcription	Spleen	Spleen

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