Variant report

Variant	rs12912007
Chromosome Location	chr15:57411492-57411493
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57410833..57413680-chr15:57416630..57418139,2	K562	blood:
2	chr15:57209351..57211172-chr15:57411034..57413159,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140262	Chromatin interaction
ENSG00000137871	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10518894	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10518895	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11071305	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11635645	0.92[ASN][1000 genomes]
rs11636100	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11636201	0.81[EUR][1000 genomes]
rs11636348	0.81[EUR][1000 genomes]
rs11852340	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11853331	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11855648	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12898327	0.85[EUR][1000 genomes]
rs12898844	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12899904	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12900038	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12900589	0.83[ASN][1000 genomes]
rs12903578	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12904070	0.88[AMR][1000 genomes]
rs12905900	0.80[EUR][1000 genomes]
rs12909402	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12910094	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12910170	0.91[ASN][1000 genomes]
rs12914182	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12914410	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12915473	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12917247	0.81[EUR][1000 genomes]
rs13313455	0.84[ASN][1000 genomes]
rs1430823	0.80[EUR][1000 genomes]
rs17819700	0.88[AMR][1000 genomes]
rs2169465	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2169466	0.91[ASN][1000 genomes]
rs2414491	0.82[EUR][1000 genomes]
rs2414494	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2615231	0.84[ASN][1000 genomes]
rs2733307	0.92[ASN][1000 genomes]
rs2733332	0.82[ASN][1000 genomes]
rs28414972	0.83[ASN][1000 genomes]
rs28514688	0.83[ASN][1000 genomes]
rs28648502	0.84[ASN][1000 genomes]
rs2927189	0.82[ASN][1000 genomes]
rs2957591	0.83[ASN][1000 genomes]
rs4774910	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62022988	0.80[EUR][1000 genomes]
rs6493901	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7168387	0.83[ASN][1000 genomes]
rs7170133	0.88[AMR][1000 genomes]
rs745652	0.81[EUR][1000 genomes]
rs8037901	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs967514	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042486	chr15:57094598-57505992	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats 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	21 gene(s)	inside rSNPs	diseases
2	nsv904251	chr15:57241970-57575916	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12912007	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57374800-57414600	Weak transcription	Fetal Kidney	kidney
2	chr15:57381000-57412400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr15:57382600-57423800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr15:57382800-57419600	Weak transcription	K562	blood
5	chr15:57386400-57426600	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr15:57386600-57424600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr15:57387000-57430000	Weak transcription	Placenta	Placenta
8	chr15:57387200-57425400	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr15:57387600-57442400	Weak transcription	Fetal Intestine Large	intestine
10	chr15:57397800-57416600	Weak transcription	Fetal Stomach	stomach
11	chr15:57398000-57415800	Weak transcription	Fetal Intestine Small	intestine
12	chr15:57399400-57424600	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr15:57399600-57416200	Weak transcription	Primary T cells from cord blood	blood
14	chr15:57402600-57414600	Weak transcription	Primary B cells from cord blood	blood
15	chr15:57403000-57424600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr15:57403800-57425200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr15:57404600-57425000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr15:57404800-57415600	Weak transcription	Thymus	Thymus
19	chr15:57406800-57413000	Weak transcription	Gastric	stomach
20	chr15:57406800-57413000	Weak transcription	Left Ventricle	heart
21	chr15:57406800-57413000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr15:57406800-57414200	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr15:57406800-57414600	Weak transcription	Colon Smooth Muscle	Colon
24	chr15:57406800-57416200	Weak transcription	Fetal Muscle Leg	muscle
25	chr15:57406800-57425000	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr15:57406800-57425400	Weak transcription	Pancreas	Pancrea
27	chr15:57406800-57425600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr15:57406800-57425600	Weak transcription	Fetal Muscle Trunk	muscle
29	chr15:57406800-57426400	Weak transcription	Colonic Mucosa	Colon
30	chr15:57406800-57426600	Weak transcription	Psoas Muscle	Psoas
31	chr15:57407000-57413600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr15:57407400-57412600	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr15:57407400-57413200	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr15:57407600-57425600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr15:57408200-57412800	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr15:57408200-57413200	Weak transcription	Small Intestine	intestine
37	chr15:57408400-57414400	Weak transcription	Stomach Mucosa	stomach
38	chr15:57409200-57414000	Enhancers	Brain Substantia Nigra	brain
39	chr15:57409400-57412200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr15:57409400-57412600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr15:57409400-57415600	Enhancers	Brain Hippocampus Middle	brain
42	chr15:57409600-57411600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr15:57409600-57412800	Enhancers	Brain Angular Gyrus	brain
44	chr15:57409800-57412200	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr15:57409800-57412400	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr15:57410000-57411800	Enhancers	Primary hematopoietic stem cells	blood
47	chr15:57410000-57412600	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr15:57410200-57412000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr15:57410200-57412400	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr15:57410200-57414800	Enhancers	ES-I3 Cell Line	embryonic stem cell

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