Variant report

Variant	rs12582584
Chromosome Location	chr12:9824138-9824139
allele	G/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	POLR2A	chr12:9821988-9824509	GM12892	blood:	n/a	n/a
2	POLR2A	chr12:9822858-9827605	GM12891	blood:	n/a	n/a
3	POLR2A	chr12:9824001-9825615	GM12892	blood:	n/a	n/a
4	POLR2A	chr12:9822918-9824346	GM15510	blood:	n/a	n/a
5	POLR2A	chr12:9824013-9825395	GM12892	blood:	n/a	n/a
6	POLR2A	chr12:9821170-9825303	GM18505	blood:	n/a	n/a
7	POLR2A	chr12:9823968-9827308	GM12892	blood:	n/a	n/a
8	POLR2A	chr12:9822835-9827266	GM12892	blood:	n/a	n/a
9	POLR2A	chr12:9824036-9827274	GM12878	blood:	n/a	n/a
10	POLR2A	chr12:9824053-9824370	GM12878	blood:	n/a	n/a
11	POLR2A	chr12:9824026-9824408	GM12891	blood:	n/a	n/a
12	MTA3	chr12:9823995-9825157	GM12878	blood:	n/a	n/a
13	POLR2A	chr12:9821389-9827321	Raji	blood:	n/a	n/a
14	POLR2A	chr12:9821973-9825071	GM18526	blood:	n/a	n/a
15	RUNX3	chr12:9824010-9824417	GM12878	blood:	n/a	n/a
16	POLR2A	chr12:9821415-9825168	GM19099	blood:	n/a	n/a
17	POLR2A	chr12:9822121-9825157	GM12878	blood:	n/a	n/a
18	POLR2A	chr12:9821330-9825306	GM19193	blood:	n/a	n/a
19	BCLAF1	chr12:9823996-9824571	GM12878	blood:	n/a	n/a
20	POLR2A	chr12:9822019-9825153	GM18951	blood:	n/a	n/a
21	POLR2A	chr12:9822941-9827304	GM12878	blood:	n/a	n/a
22	POLR2A	chr12:9822886-9827320	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:9799292..9802850-chr12:9823422..9827161,3	MCF-7	breast:

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

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1044771	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1056151	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10772046	0.85[ASN][1000 genomes]
rs10772062	0.82[ASN][1000 genomes]
rs10844456	0.85[ASN][1000 genomes]
rs10844468	0.85[ASN][1000 genomes]
rs10844472	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844503	0.85[ASN][1000 genomes]
rs10844537	0.84[ASN][1000 genomes]
rs10844562	0.82[ASN][1000 genomes]
rs11052372	0.87[ASN][1000 genomes]
rs11052423	0.85[ASN][1000 genomes]
rs11052426	0.85[ASN][1000 genomes]
rs11052497	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052552	0.87[ASN][1000 genomes]
rs11052582	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11052604	0.84[ASN][1000 genomes]
rs12227655	0.82[ASN][1000 genomes]
rs12228641	0.81[ASN][1000 genomes]
rs12424826	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12427310	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1560011	0.87[ASN][1000 genomes]
rs17806710	0.85[ASN][1000 genomes]
rs1985788	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2012643	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2080206	0.91[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2080211	0.99[ASN][1000 genomes]
rs2098298	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2114870	0.81[ASN][1000 genomes]
rs2114871	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2268146	0.80[ASN][1000 genomes]
rs2894	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2895988	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764021	0.87[ASN][1000 genomes]
rs3764022	0.85[ASN][1000 genomes]
rs4763283	0.88[ASN][1000 genomes]
rs4763839	0.87[ASN][1000 genomes]
rs4763840	0.88[ASN][1000 genomes]
rs61915472	0.94[AFR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61915473	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7310460	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs741200	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7960328	0.94[AFR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7964018	0.92[ASN][1000 genomes]
rs7968401	0.85[ASN][1000 genomes]
rs7974396	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7977720	0.83[ASN][1000 genomes]
rs7977940	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs917913	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9332411	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[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	nsv427903	chr12:9371593-9830668	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	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
3	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
4	esv1821732	chr12:9560087-9830668	Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv1823760	chr12:9560087-9830668	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv428271	chr12:9560087-9830668	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12582584	CLECL1	cis	Nerve Tibial	GTEx
rs12582584	CLECL1	Cis_1M	lymphoblastoid	RTeQTL
rs12582584	CLEC2D	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9802400-9849800	Weak transcription	Pancreas	Pancrea
2	chr12:9803600-9826200	Weak transcription	Esophagus	oesophagus
3	chr12:9807000-9826000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr12:9807600-9847200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr12:9812800-9825800	Weak transcription	Right Ventricle	heart
6	chr12:9813000-9825800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr12:9813000-9826200	Weak transcription	Brain Anterior Caudate	brain
8	chr12:9813000-9826200	Weak transcription	Gastric	stomach
9	chr12:9813800-9826000	Weak transcription	NHDF-Ad	bronchial
10	chr12:9815000-9826000	Weak transcription	Lung	lung
11	chr12:9815000-9826000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr12:9815000-9826200	Weak transcription	Colonic Mucosa	Colon
13	chr12:9815000-9826200	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr12:9815000-9826400	Weak transcription	Fetal Intestine Small	intestine
15	chr12:9815200-9825000	Weak transcription	K562	blood
16	chr12:9815200-9825800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr12:9815200-9825800	Weak transcription	Colon Smooth Muscle	Colon
18	chr12:9815200-9826200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr12:9815200-9828400	Weak transcription	Liver	Liver
20	chr12:9815200-9840600	Weak transcription	Fetal Brain Male	brain
21	chr12:9815200-9841600	Weak transcription	Fetal Kidney	kidney
22	chr12:9815400-9825000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr12:9815400-9825600	Weak transcription	HepG2	liver
24	chr12:9815600-9825200	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr12:9815600-9825600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr12:9815600-9825800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr12:9815600-9826000	Weak transcription	Spleen	Spleen
28	chr12:9815600-9833800	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr12:9815800-9825600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr12:9816200-9832600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr12:9816200-9840600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr12:9817000-9826000	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr12:9817200-9824800	Weak transcription	Dnd41	blood
34	chr12:9817200-9837800	Weak transcription	Aorta	Aorta
35	chr12:9817600-9825400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr12:9817600-9826400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr12:9818000-9825800	Weak transcription	Fetal Muscle Leg	muscle
38	chr12:9818000-9825800	Weak transcription	Placenta	Placenta
39	chr12:9818000-9826000	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr12:9818000-9826000	Weak transcription	Fetal Stomach	stomach
41	chr12:9818000-9826000	Weak transcription	Left Ventricle	heart
42	chr12:9818000-9826200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr12:9818000-9839200	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr12:9818000-9839800	Weak transcription	Ovary	ovary
45	chr12:9818000-9840000	Weak transcription	Fetal Intestine Large	intestine
46	chr12:9818000-9849800	Weak transcription	Brain Germinal Matrix	brain
47	chr12:9818200-9825600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr12:9818200-9826200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr12:9818200-9826400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr12:9818200-9828600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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