Variant report

Variant	rs12961711
Chromosome Location	chr18:12707767-12707768
allele	A/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	STAT3	chr18:12707575-12707873	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:12699736..12702348-chr18:12705277..12708356,3	K562	blood:
2	chr18:12707453..12709130-chr18:12712396..12714516,2	MCF-7	breast:
3	chr18:12706059..12708008-chr18:12949881..12951466,2	K562	blood:
4	chr18:12700615..12704798-chr18:12705051..12713643,12	MCF-7	breast:
5	chr18:12693359..12696587-chr18:12706551..12708313,3	K562	blood:

Variant related genes	Relation type
CEP76	TF binding region
ENSG00000128789	Chromatin interaction
ENSG00000101624	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1105748	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12954350	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12954606	1.00[ASN][1000 genomes]
rs12955162	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12955176	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12956026	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12956686	1.00[ASN][1000 genomes]
rs12957011	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12957283	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12958301	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12958598	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12959199	1.00[CEU][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12961307	1.00[ASN][1000 genomes]
rs12963149	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12964717	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12965549	1.00[CEU][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12966082	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12966571	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12967250	1.00[ASN][1000 genomes]
rs12970939	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17525318	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17525459	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17525599	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17615525	1.00[ASN][1000 genomes]
rs17615801	1.00[ASN][1000 genomes]
rs17615991	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17616124	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34054541	1.00[ASN][1000 genomes]
rs34084006	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34088731	1.00[ASN][1000 genomes]
rs34180475	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34183067	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34229934	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34371240	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34460164	1.00[ASN][1000 genomes]
rs34503700	1.00[ASN][1000 genomes]
rs34737110	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34859829	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34923819	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34933611	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35082337	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35160505	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35190325	1.00[ASN][1000 genomes]
rs35280383	1.00[ASN][1000 genomes]
rs35309605	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35612342	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35616981	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35643117	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs35686128	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35744165	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35815040	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35826479	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35864675	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35939870	1.00[ASN][1000 genomes]
rs4510091	1.00[ASN][1000 genomes]
rs45541436	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71351491	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs71351492	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs71351494	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs71351495	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs71351501	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs71353221	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs71353222	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71363149	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	esv3528039	chr18:12396582-12851293	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	esv3528041	chr18:12396641-12851245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv523743	chr18:12474505-12742809	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv1820040	chr18:12635601-12725236	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	esv1817845	chr18:12635601-12733705	Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	esv1821625	chr18:12635601-12733705	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
10	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
11	nsv1064273	chr18:12697601-12828251	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12961711	RP11-861E21.2	cis	Thyroid	GTEx
rs12961711	SPIRE1	cis	Thyroid	GTEx
rs12961711	CEP76	Cis_1M	lymphoblastoid	RTeQTL
rs12961711	SLMO1	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12703400-12709000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr18:12703800-12713200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr18:12704200-12709600	Weak transcription	HSMMtube	muscle
4	chr18:12704200-12709800	Weak transcription	Right Ventricle	heart
5	chr18:12704200-12713000	Weak transcription	Aorta	Aorta
6	chr18:12704200-12713200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr18:12704200-12713200	Weak transcription	Psoas Muscle	Psoas
8	chr18:12704200-12726800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr18:12704400-12710000	Weak transcription	NHLF	lung
10	chr18:12704600-12708400	Weak transcription	Gastric	stomach
11	chr18:12704600-12713000	Weak transcription	Pancreas	Pancrea
12	chr18:12704800-12727200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr18:12704800-12727800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr18:12705000-12710400	Weak transcription	Small Intestine	intestine
15	chr18:12705000-12722400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr18:12705000-12725200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr18:12705000-12728600	Weak transcription	Stomach Mucosa	stomach
18	chr18:12705400-12708000	Strong transcription	HSMM	muscle
19	chr18:12705400-12714600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr18:12705400-12726000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr18:12705400-12727200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr18:12705600-12707800	Strong transcription	Primary B cells from cord blood	blood
23	chr18:12705600-12708400	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr18:12705600-12708800	Strong transcription	NHEK	skin
25	chr18:12705600-12711000	Strong transcription	Primary hematopoietic stem cells	blood
26	chr18:12705600-12711400	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr18:12705600-12711800	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr18:12705600-12726000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr18:12705600-12727000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr18:12705600-12727200	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr18:12705600-12727200	Strong transcription	Duodenum Mucosa	Duodenum
32	chr18:12705600-12727200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr18:12705800-12708400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr18:12705800-12708600	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr18:12705800-12711000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr18:12705800-12712600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr18:12705800-12713200	Weak transcription	Fetal Brain Male	brain
38	chr18:12705800-12714800	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr18:12705800-12726600	Strong transcription	Fetal Thymus	thymus
40	chr18:12705800-12727000	Strong transcription	Placenta	Placenta
41	chr18:12705800-12727200	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr18:12705800-12727200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr18:12705800-12727200	Strong transcription	Fetal Muscle Leg	muscle
44	chr18:12706000-12708200	Strong transcription	NH-A	brain
45	chr18:12706000-12708400	Strong transcription	Brain Germinal Matrix	brain
46	chr18:12706000-12714200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr18:12706000-12727000	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr18:12706000-12727200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr18:12706200-12708600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
50	chr18:12706200-12716000	Strong transcription	Fetal Lung	lung

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