Variant report

Variant	rs34859829
Chromosome Location	chr18:12687138-12687139
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:12685127..12688617-chr18:12697968..12702228,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101624	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 4 )

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

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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12956026	0.96[AMR][1000 genomes];0.96[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];1.00[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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12959199	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12959998	1.00[ASN][1000 genomes]
rs12961307	1.00[ASN][1000 genomes]
rs12961711	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12963149	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12964717	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12965549	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12966082	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12966571	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[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]
rs17524639	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];1.00[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];0.99[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]
rs34923819	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[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];1.00[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];1.00[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];0.98[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];0.98[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];0.98[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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71351485	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];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71363149	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	esv1791969	chr18:12643193-12697711	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs34859829	RP11-861E21.2	cis	Thyroid	GTEx
rs34859829	SLMO1	cis	Artery Tibial	GTEx
rs34859829	SPIRE1	cis	Thyroid	GTEx
rs34859829	CEP76	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12658800-12701800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr18:12659000-12700200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr18:12660000-12692600	Weak transcription	Brain Cingulate Gyrus	brain
4	chr18:12660400-12700800	Weak transcription	Fetal Brain Male	brain
5	chr18:12662800-12701600	Weak transcription	Aorta	Aorta
6	chr18:12667000-12701600	Weak transcription	Gastric	stomach
7	chr18:12668400-12694800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr18:12669200-12694200	Weak transcription	A549	lung
9	chr18:12669800-12694200	Weak transcription	Hela-S3	cervix
10	chr18:12672200-12701400	Weak transcription	Colonic Mucosa	Colon
11	chr18:12672400-12687400	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr18:12672400-12697200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr18:12673200-12701600	Weak transcription	Psoas Muscle	Psoas
14	chr18:12674200-12693800	Weak transcription	NHEK	skin
15	chr18:12674600-12693800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr18:12674600-12701600	Weak transcription	Right Ventricle	heart
17	chr18:12674600-12701600	Weak transcription	Small Intestine	intestine
18	chr18:12674800-12700600	Weak transcription	Brain Substantia Nigra	brain
19	chr18:12674800-12701400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr18:12675000-12694000	Weak transcription	Stomach Mucosa	stomach
21	chr18:12678200-12701400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr18:12678400-12692400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr18:12678400-12692400	Weak transcription	Left Ventricle	heart
24	chr18:12678400-12693800	Weak transcription	HMEC	breast
25	chr18:12678400-12694200	Weak transcription	Placenta	Placenta
26	chr18:12678400-12696800	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr18:12678400-12701200	Weak transcription	NH-A	brain
28	chr18:12678400-12701600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr18:12678400-12701600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr18:12678400-12701600	Weak transcription	HSMMtube	muscle
31	chr18:12679600-12687200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr18:12679600-12687400	Weak transcription	Spleen	Spleen
33	chr18:12679600-12693800	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr18:12679600-12693800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr18:12679600-12696600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr18:12679600-12698400	Weak transcription	Duodenum Mucosa	Duodenum
37	chr18:12679600-12698400	Weak transcription	NHLF	lung
38	chr18:12679600-12700400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr18:12679600-12700400	Weak transcription	Colon Smooth Muscle	Colon
40	chr18:12679600-12700600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr18:12679600-12701000	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr18:12679600-12701000	Weak transcription	Rectal Smooth Muscle	rectum
43	chr18:12679600-12701200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr18:12679600-12701600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr18:12679800-12692400	Weak transcription	Brain Angular Gyrus	brain
46	chr18:12679800-12698800	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr18:12679800-12701000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr18:12679800-12701000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr18:12679800-12701000	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr18:12680000-12687200	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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