Variant report

Variant	rs1211277
Chromosome Location	chr12:105502841-105502842
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	POLR2A	chr12:105502732-105502910	HepG2	liver:	n/a	n/a
2	MXI1	chr12:105500112-105503958	SK-N-SH	brain:	n/a	n/a
3	GATA3	chr12:105502808-105503488	SK-N-SH	brain:	n/a	chr12:105503263-105503279 chr12:105503267-105503274 chr12:105503260-105503281 chr12:105503267-105503274 chr12:105503267-105503274 chr12:105503266-105503276 chr12:105503264-105503274
4	PBX3	chr12:105502796-105503434	SK-N-SH	brain:	n/a	n/a
5	HCFC1	chr12:105500332-105502938	Hela-S3	cervix:	n/a	n/a
6	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
7	GTF3C2	chr12:105502063-105503078	Hela-S3	cervix:	n/a	n/a
8	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
9	FOSL2	chr12:105502824-105503437	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr12:105502744-105504120	HUVEC	blood vessel:	n/a	n/a
11	YY1	chr12:105502747-105502960	K562	blood:	n/a	n/a
12	RCOR1	chr12:105501010-105502862	K562	blood:	n/a	n/a
13	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	chr12:105502740..105505259-chr12:105518776..105521182,3	K562	blood:
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	chr12:105228136..105230854-chr12:105501668..105503168,2	MCF-7	breast:
11	chr12:105477772..105479851-chr12:105501425..105505225,4	MCF-7	breast:
12	chr12:105501229..105503953-chr12:105621352..105624637,3	MCF-7	breast:
13	chr12:104521574..104524477-chr12:105501454..105503015,2	MCF-7	breast:
14	chr12:104678772..104682731-chr12:105498551..105503490,6	K562	blood:
15	chr12:105500023..105504653-chr12:105628064..105630551,4	K562	blood:
16	chr12:105502302..105504240-chr12:105518371..105521182,2	K562	blood:

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

Extended variants
information (count: 124 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs10746010	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778367	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778368	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778369	0.86[EUR][1000 genomes]
rs1107755	0.83[EUR][1000 genomes]
rs1107757	0.83[EUR][1000 genomes]
rs11112424	0.83[EUR][1000 genomes]
rs11112434	0.83[EUR][1000 genomes]
rs1196742	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196745	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196748	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196749	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196753	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196754	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196756	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196759	1.00[ASN][1000 genomes]
rs1196760	1.00[ASN][1000 genomes]
rs1196764	0.99[EUR][1000 genomes]
rs1196765	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196770	0.92[EUR][1000 genomes]
rs1196772	0.92[EUR][1000 genomes]
rs1196777	0.91[EUR][1000 genomes]
rs1196780	0.84[EUR][1000 genomes]
rs1196782	0.83[EUR][1000 genomes]
rs1196786	0.83[EUR][1000 genomes]
rs1196787	0.82[EUR][1000 genomes]
rs1196789	0.82[EUR][1000 genomes]
rs1196793	0.83[EUR][1000 genomes]
rs1196795	0.81[EUR][1000 genomes]
rs1196797	0.83[EUR][1000 genomes]
rs1196798	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1196800	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196801	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196805	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196806	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196807	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196808	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196811	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1196813	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196817	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196819	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196820	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196823	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196825	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196831	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196833	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196834	0.83[EUR][1000 genomes]
rs1196839	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196841	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196842	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196844	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196847	0.85[EUR][1000 genomes]
rs1196848	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196851	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1196853	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196857	1.00[ASN][1000 genomes]
rs1196859	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196861	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196862	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196864	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196869	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1196871	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196872	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1196873	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1196874	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196881	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196884	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196885	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1206559	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1209308	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1209637	0.82[EUR][1000 genomes]
rs1211276	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1211626	0.83[EUR][1000 genomes]
rs12369709	0.82[EUR][1000 genomes]
rs12814458	0.83[EUR][1000 genomes]
rs12816560	0.84[EUR][1000 genomes]
rs1345096	0.89[EUR][1000 genomes]
rs1444610	0.82[EUR][1000 genomes]
rs1621553	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1663564	1.00[ASN][1000 genomes]
rs1663565	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1732370	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2166142	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2246243	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2257156	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2374449	0.88[EUR][1000 genomes]
rs2440692	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2440714	0.95[EUR][1000 genomes]
rs2440715	1.00[ASN][1000 genomes]
rs2440718	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2464173	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2464175	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2464181	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2464182	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35679386	0.84[EUR][1000 genomes]
rs4356312	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4356313	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4372534	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4390426	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964122	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964331	0.88[EUR][1000 genomes]
rs6539183	0.84[EUR][1000 genomes]
rs6539186	0.85[EUR][1000 genomes]
rs6539187	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6539188	0.88[EUR][1000 genomes]
rs7132040	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132624	0.90[EUR][1000 genomes]
rs7132855	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs71441895	0.92[EUR][1000 genomes]
rs7299701	0.87[EUR][1000 genomes]
rs7302854	0.85[EUR][1000 genomes]
rs7303961	0.92[EUR][1000 genomes]
rs73181823	0.84[EUR][1000 genomes]
rs7963877	0.84[EUR][1000 genomes]
rs873119	0.84[EUR][1000 genomes]
rs935240	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935241	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935242	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935244	0.92[EUR][1000 genomes]
rs935246	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935248	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs935249	0.97[AMR][1000 genomes];0.98[EUR][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1211277	ALDH1L2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105500200-105503000	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr12:105500200-105504000	Active TSS	Brain Anterior Caudate	brain
3	chr12:105500400-105503200	Active TSS	Brain Angular Gyrus	brain
4	chr12:105500400-105503400	Active TSS	Stomach Smooth Muscle	stomach
5	chr12:105500400-105503800	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr12:105500400-105504600	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr12:105500400-105505000	Active TSS	K562	blood
8	chr12:105500600-105503000	Active TSS	Brain Cingulate Gyrus	brain
9	chr12:105500600-105503000	Active TSS	Fetal Kidney	kidney
10	chr12:105500600-105503200	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr12:105500600-105503200	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr12:105500600-105503400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr12:105500600-105503400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr12:105500600-105503600	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr12:105500600-105503600	Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr12:105500600-105503800	Active TSS	H1 Cell Line	embryonic stem cell
17	chr12:105500600-105503800	Active TSS	Colonic Mucosa	Colon
18	chr12:105500600-105503800	Active TSS	HSMMtube	muscle
19	chr12:105500600-105504200	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr12:105500800-105503000	Active TSS	Fetal Brain Male	brain
21	chr12:105500800-105503000	Active TSS	Rectal Smooth Muscle	rectum
22	chr12:105500800-105503400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr12:105500800-105503400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr12:105500800-105503400	Active TSS	Brain Hippocampus Middle	brain
25	chr12:105500800-105503400	Active TSS	Left Ventricle	heart
26	chr12:105500800-105503400	Active TSS	Ovary	ovary
27	chr12:105500800-105503400	Active TSS	Psoas Muscle	Psoas
28	chr12:105500800-105503400	Active TSS	Right Atrium	heart
29	chr12:105500800-105503400	Active TSS	HSMM	muscle
30	chr12:105500800-105503400	Active TSS	NHDF-Ad	bronchial
31	chr12:105500800-105503600	Active TSS	H9 Cell Line	embryonic stem cell
32	chr12:105500800-105503600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:105500800-105503600	Active TSS	Primary B cells from peripheral blood	blood
34	chr12:105500800-105503600	Active TSS	Fetal Intestine Large	intestine
35	chr12:105500800-105503600	Active TSS	Fetal Intestine Small	intestine
36	chr12:105500800-105503600	Active TSS	Right Ventricle	heart
37	chr12:105500800-105503800	Active TSS	A549	lung
38	chr12:105500800-105504000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
39	chr12:105500800-105504400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr12:105500800-105504800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr12:105501000-105503000	Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr12:105501000-105503000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
43	chr12:105501000-105503000	Active TSS	Sigmoid Colon	Sigmoid Colon
44	chr12:105501000-105503000	Active TSS	Small Intestine	intestine
45	chr12:105501000-105503200	Active TSS	HMEC	breast
46	chr12:105501000-105503400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr12:105501000-105503400	Active TSS	Primary monocytes fromperipheralblood	blood
48	chr12:105501000-105503400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr12:105501000-105503400	Active TSS	Lung	lung
50	chr12:105501000-105503400	Active TSS	Rectal Mucosa Donor 29	rectum

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