Variant report

Variant	rs7964184
Chromosome Location	chr12:105593592-105593593
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	chr12:105593357-105593592	Hela-S3	cervix:	n/a	n/a
2	FOS	chr12:105593260-105593656	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr12:105593271-105593618	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr12:105593279-105593612	MCF10A-Er-Src	breast:	n/a	n/a
5	MYC	chr12:105593239-105593600	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr12:105593253-105593613	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:105592344..105594615-chr12:105595221..105597389,2	MCF-7	breast:
2	chr12:105501608..105503179-chr12:105592060..105594445,2	K562	blood:
3	chr12:105592769..105599626-chr12:105599908..105606799,7	MCF-7	breast:

Variant related genes	Relation type
APPL2	TF binding region
ENSG00000136044	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10082824	1.00[ASN][1000 genomes]
rs10083185	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112315	1.00[ASN][1000 genomes]
rs11112316	1.00[ASN][1000 genomes]
rs11112318	1.00[ASN][1000 genomes]
rs11112333	1.00[ASN][1000 genomes]
rs11112381	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112389	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112410	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11495192	1.00[ASN][1000 genomes]
rs11559871	0.85[EUR][1000 genomes]
rs11829598	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12299366	0.92[EUR][1000 genomes]
rs12299391	0.92[EUR][1000 genomes]
rs12301914	0.92[EUR][1000 genomes]
rs12304384	0.92[EUR][1000 genomes]
rs12305766	0.85[EUR][1000 genomes]
rs12307372	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12311156	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12312965	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12317637	0.87[EUR][1000 genomes]
rs12317804	0.92[EUR][1000 genomes]
rs12321199	0.92[EUR][1000 genomes]
rs12321518	0.89[EUR][1000 genomes]
rs12321534	0.82[EUR][1000 genomes]
rs12369202	1.00[ASN][1000 genomes]
rs12372454	1.00[ASN][1000 genomes]
rs12424191	0.89[EUR][1000 genomes]
rs12424709	0.89[EUR][1000 genomes]
rs12425803	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17036595	1.00[ASN][1000 genomes]
rs17036608	1.00[ASN][1000 genomes]
rs1801070	1.00[ASN][1000 genomes]
rs35149056	1.00[ASN][1000 genomes]
rs3910856	1.00[ASN][1000 genomes]
rs55679730	1.00[ASN][1000 genomes]
rs56284118	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56862143	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59320697	0.89[EUR][1000 genomes]
rs59593474	0.92[EUR][1000 genomes]
rs60835294	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60999193	0.92[EUR][1000 genomes]
rs6539184	1.00[ASN][1000 genomes]
rs7132816	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7133728	0.96[EUR][1000 genomes]
rs7136453	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7138574	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7300130	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7302842	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7305406	0.89[EUR][1000 genomes]
rs7313309	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7315964	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73179946	1.00[ASN][1000 genomes]
rs73179970	1.00[ASN][1000 genomes]
rs73179974	1.00[ASN][1000 genomes]
rs73179990	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73179996	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73179998	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73180001	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73181822	0.89[EUR][1000 genomes]
rs73181857	0.85[EUR][1000 genomes]
rs73193630	1.00[ASN][1000 genomes]
rs73193631	1.00[ASN][1000 genomes]
rs7956643	1.00[ASN][1000 genomes]
rs7971630	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7975787	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7978034	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	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
2	nsv455704	chr12:105583877-105651356	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
3	nsv560053	chr12:105583877-105651356	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105546800-105625200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:105558800-105615200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:105561400-105598400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr12:105571400-105617800	Weak transcription	K562	blood
5	chr12:105576000-105595600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr12:105576400-105606000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr12:105577000-105607200	Strong transcription	Sigmoid Colon	Sigmoid Colon
8	chr12:105577400-105593600	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr12:105577400-105616200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr12:105577800-105594200	Strong transcription	Fetal Intestine Large	intestine
11	chr12:105577800-105594400	Strong transcription	Skeletal Muscle Female	skeletal muscle
12	chr12:105577800-105595200	Strong transcription	Left Ventricle	heart
13	chr12:105577800-105598600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr12:105577800-105598800	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr12:105577800-105599400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:105577800-105602600	Strong transcription	Fetal Thymus	thymus
17	chr12:105577800-105603600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr12:105577800-105605400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr12:105577800-105605600	Strong transcription	Primary B cells from cord blood	blood
20	chr12:105577800-105607400	Strong transcription	Duodenum Mucosa	Duodenum
21	chr12:105578000-105599200	Strong transcription	Rectal Mucosa Donor 31	rectum
22	chr12:105578000-105607400	Strong transcription	Fetal Brain Female	brain
23	chr12:105578000-105623200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr12:105578200-105593600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr12:105578200-105620000	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr12:105578400-105602400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr12:105579000-105598600	Strong transcription	HSMM	muscle
28	chr12:105579000-105605200	Strong transcription	Fetal Muscle Leg	muscle
29	chr12:105579000-105612400	Strong transcription	Stomach Smooth Muscle	stomach
30	chr12:105579400-105595000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr12:105579800-105596000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr12:105580200-105613200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:105581200-105602600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr12:105581200-105605400	Strong transcription	Fetal Muscle Trunk	muscle
35	chr12:105581400-105595000	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr12:105581800-105602600	Strong transcription	Skeletal Muscle Male	skeletal muscle
37	chr12:105581800-105605200	Strong transcription	Brain Germinal Matrix	brain
38	chr12:105582000-105595000	Strong transcription	Ovary	ovary
39	chr12:105582000-105600200	Strong transcription	Fetal Stomach	stomach
40	chr12:105582000-105602600	Strong transcription	Lung	lung
41	chr12:105582000-105603400	Strong transcription	Spleen	Spleen
42	chr12:105582600-105596000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr12:105582800-105594000	Strong transcription	Fetal Intestine Small	intestine
44	chr12:105582800-105598200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr12:105582800-105602600	Strong transcription	Thymus	Thymus
46	chr12:105583600-105602600	Strong transcription	Esophagus	oesophagus
47	chr12:105583600-105605600	Strong transcription	Right Ventricle	heart
48	chr12:105584000-105627000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr12:105584400-105600200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr12:105585400-105603400	Strong transcription	HSMMtube	muscle

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