Variant report

Variant	rs10431460
Chromosome Location	chr12:105502645-105502646
allele	C/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	MXI1	chr12:105500112-105503958	SK-N-SH	brain:	n/a	n/a
2	MAX	chr12:105502449-105502757	Hela-S3	cervix:	n/a	n/a
3	HCFC1	chr12:105500332-105502938	Hela-S3	cervix:	n/a	n/a
4	GATA2	chr12:105502431-105503300	HUVEC	blood vessel:	n/a	chr12:105502451-105502461 chr12:105503263-105503279 chr12:105502452-105502459 chr12:105503267-105503274 chr12:105503260-105503281 chr12:105502448-105502464 chr12:105503267-105503274 chr12:105502445-105502466 chr12:105503267-105503274 chr12:105503266-105503276 chr12:105502452-105502459 chr12:105502452-105502459 chr12:105502452-105502461 chr12:105503264-105503274
5	GTF3C2	chr12:105502063-105503078	Hela-S3	cervix:	n/a	n/a
6	GATA2	chr12:105500959-105502952	SH-SY5Y	brain:	n/a	chr12:105502451-105502461 chr12:105502452-105502459 chr12:105502448-105502464 chr12:105502445-105502466 chr12:105502079-105502089 chr12:105502452-105502459 chr12:105502452-105502459 chr12:105502452-105502461
7	MXI1	chr12:105500731-105502681	IMR90	lung:	n/a	n/a
8	POLR2A	chr12:105502441-105502650	MCF10A-Er-Src	breast:	n/a	n/a
9	GATA3	chr12:105500827-105502757	A549	lung:	n/a	chr12:105502451-105502461 chr12:105502452-105502459 chr12:105502451-105502459 chr12:105502448-105502464 chr12:105502445-105502466 chr12:105502079-105502089 chr12:105502452-105502459 chr12:105502452-105502459 chr12:105502452-105502461
10	RCOR1	chr12:105501010-105502862	K562	blood:	n/a	n/a
11	GATA3	chr12:105501021-105503575	SK-N-SH	brain:	n/a	chr12:105502451-105502461 chr12:105503263-105503279 chr12:105502452-105502459 chr12:105503267-105503274 chr12:105502451-105502459 chr12:105503260-105503281 chr12:105502448-105502464 chr12:105503267-105503274 chr12:105502445-105502466 chr12:105503267-105503274 chr12:105503266-105503276 chr12:105502079-105502089 chr12:105502452-105502459 chr12:105502452-105502459 chr12:105502452-105502461 chr12:105503264-105503274

No.	Distal block	Cell Line	Cell type
1	chr12:105476808..105479481-chr12:105501524..105503382,3	K562	blood:
2	chr12:105500524..105503114-chr12:106640734..106642263,2	MCF-7	breast:
3	chr12:105501608..105503179-chr12:105592060..105594445,2	K562	blood:
4	chr12:105476762..105478986-chr12:105499431..105503042,4	K562	blood:
5	chr12:105501540..105503183-chr12:105627693..105630661,2	MCF-7	breast:
6	chr12:104530239..104532383-chr12:105499797..105502736,2	MCF-7	breast:
7	chr12:104681104..104682731-chr12:105500276..105502937,2	K562	blood:
8	chr12:105499144..105502991-chr12:105627617..105631044,5	MCF-7	breast:
9	chr12:105477899..105479847-chr12:105501301..105502988,2	MCF-7	breast:
10	chr12:105379411..105381004-chr12:105501090..105502694,2	MCF-7	breast:
11	chr12:105228136..105230854-chr12:105501668..105503168,2	MCF-7	breast:
12	chr12:105477772..105479851-chr12:105501425..105505225,4	MCF-7	breast:
13	chr12:105501229..105503953-chr12:105621352..105624637,3	MCF-7	breast:
14	chr12:104521574..104524477-chr12:105501454..105503015,2	MCF-7	breast:
15	chr12:104678772..104682731-chr12:105498551..105503490,6	K562	blood:
16	chr12:105500023..105504653-chr12:105628064..105630551,4	K562	blood:
17	chr12:105502302..105504240-chr12:105518371..105521182,2	K562	blood:

Variant related genes	Relation type
ENSG00000257999	TF binding region
ENSG00000136010	Chromatin interaction
ENSG00000151131	Chromatin interaction
ENSG00000120837	Chromatin interaction
ENSG00000258355	Chromatin interaction
ENSG00000136026	Chromatin interaction
ENSG00000198431	Chromatin interaction
ENSG00000235162	Chromatin interaction
ENSG00000136044	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1014502	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1057110	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1077896	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10861359	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10861361	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1109433	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11112369	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11112370	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11112372	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11112375	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11112376	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112379	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112388	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11112409	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11112412	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11112415	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11112416	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11112421	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11112423	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11112432	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11831854	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11832489	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11834277	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12228093	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12228948	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12230762	0.82[ASN][1000 genomes]
rs12812433	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12815031	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12819309	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12830078	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1317955	0.86[EUR][1000 genomes]
rs1373552	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1444611	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1470381	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2272495	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2293643	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2293644	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2464176	0.93[ASN][1000 genomes]
rs28549976	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34075890	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34119882	0.80[ASN][1000 genomes]
rs34983773	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35462155	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35672903	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3736628	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3794222	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3794223	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3794224	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3794227	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3817607	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3829296	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4964125	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4964334	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4964335	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4964336	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4964338	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4964339	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4964340	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4964342	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55908437	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56693261	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73179994	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7485364	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs755604	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8015	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs881279	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9919746	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[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	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv832506	chr12:105461274-105637561	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105500200-105502800	Active TSS	Cortex derived primary cultured neurospheres	brain
2	chr12:105500200-105503000	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr12:105500200-105504000	Active TSS	Brain Anterior Caudate	brain
4	chr12:105500400-105503200	Active TSS	Brain Angular Gyrus	brain
5	chr12:105500400-105503400	Active TSS	Stomach Smooth Muscle	stomach
6	chr12:105500400-105503800	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr12:105500400-105504600	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr12:105500400-105505000	Active TSS	K562	blood
9	chr12:105500600-105503000	Active TSS	Brain Cingulate Gyrus	brain
10	chr12:105500600-105503000	Active TSS	Fetal Kidney	kidney
11	chr12:105500600-105503200	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr12:105500600-105503200	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr12:105500600-105503400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr12:105500600-105503400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr12:105500600-105503600	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr12:105500600-105503600	Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr12:105500600-105503800	Active TSS	H1 Cell Line	embryonic stem cell
18	chr12:105500600-105503800	Active TSS	Colonic Mucosa	Colon
19	chr12:105500600-105503800	Active TSS	HSMMtube	muscle
20	chr12:105500600-105504200	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr12:105500800-105502800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr12:105500800-105502800	Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr12:105500800-105502800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr12:105500800-105502800	Active TSS	Aorta	Aorta
25	chr12:105500800-105502800	Active TSS	Fetal Muscle Trunk	muscle
26	chr12:105500800-105503000	Active TSS	Fetal Brain Male	brain
27	chr12:105500800-105503000	Active TSS	Rectal Smooth Muscle	rectum
28	chr12:105500800-105503400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr12:105500800-105503400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:105500800-105503400	Active TSS	Brain Hippocampus Middle	brain
31	chr12:105500800-105503400	Active TSS	Left Ventricle	heart
32	chr12:105500800-105503400	Active TSS	Ovary	ovary
33	chr12:105500800-105503400	Active TSS	Psoas Muscle	Psoas
34	chr12:105500800-105503400	Active TSS	Right Atrium	heart
35	chr12:105500800-105503400	Active TSS	HSMM	muscle
36	chr12:105500800-105503400	Active TSS	NHDF-Ad	bronchial
37	chr12:105500800-105503600	Active TSS	H9 Cell Line	embryonic stem cell
38	chr12:105500800-105503600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr12:105500800-105503600	Active TSS	Primary B cells from peripheral blood	blood
40	chr12:105500800-105503600	Active TSS	Fetal Intestine Large	intestine
41	chr12:105500800-105503600	Active TSS	Fetal Intestine Small	intestine
42	chr12:105500800-105503600	Active TSS	Right Ventricle	heart
43	chr12:105500800-105503800	Active TSS	A549	lung
44	chr12:105500800-105504000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
45	chr12:105500800-105504400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr12:105500800-105504800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr12:105501000-105502800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr12:105501000-105502800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr12:105501000-105502800	Active TSS	Adipose Nuclei	Adipose
50	chr12:105501000-105502800	Active TSS	Spleen	Spleen

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