Variant report

Variant	rs12459634
Chromosome Location	chr19:36230174-36230175
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	chr19:36205476..36213390-chr19:36226310..36233646,27	MCF-7	breast:
2	chr19:36229002..36231040-chr19:36266877..36269774,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272333	Chromatin interaction
ENSG00000004777	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10401156	0.94[EUR][1000 genomes]
rs10402601	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10402837	0.95[EUR][1000 genomes]
rs11549030	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2239947	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2293686	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28633929	0.82[TSI][hapmap]
rs28656784	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2871921	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35729071	0.88[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.85[AFR][1000 genomes]
rs3746277	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3761087	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3848662	0.93[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs3848665	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62112162	0.84[EUR][1000 genomes]
rs7260184	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8106959	0.88[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv911630	chr19:36149761-36290977	Enhancers Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	69 gene(s)	inside rSNPs	diseases
3	nsv458566	chr19:36156588-36265508	Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
4	nsv579422	chr19:36156588-36265508	Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
5	nsv911631	chr19:36169285-36290977	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
6	nsv911632	chr19:36174176-36288297	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv911633	chr19:36206050-36283847	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
8	nsv911634	chr19:36206050-36290977	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
9	nsv543996	chr19:36210269-36265431	Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
10	nsv1057830	chr19:36210269-36279794	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
11	nsv543997	chr19:36210269-36279794	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
12	nsv911635	chr19:36217333-36283847	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
13	nsv515536	chr19:36219525-36240960	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
14	nsv458567	chr19:36221051-36283847	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
15	nsv579423	chr19:36221051-36283847	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs12459634	TMEM149	cis	brain	BrainEAC
rs12459634	TMEM149	cis	normal skin	skin_eQTL
rs12459634	TMEM149	cis	multi-tissue	Pritchard
rs12459634	U2AF1L4	cis	Muscle Skeletal	GTEx
rs12459634	UPK1A	trans	cerebellum	SCAN
rs12459634	U2AF1L4	Cis_1M	lymphoblastoid	RTeQTL
rs12459634	TMEM149	cis	lymphoblastoid	seeQTL
rs12459634	U2AF1L4	cis	lung	GTEx
rs12459634	TMEM149	cis	Brain Pons	GTEx
rs12459634	ZNF568	cis	cerebellum	SCAN
rs12459634	TMEM149	cis	brain	seeQTL
rs12459634	PSG1	cis	parietal	SCAN
rs12459634	TMEM149	Cis_1M	lymphoblastoid	RTeQTL
rs12459634	LIN37	Cis_1M	lymphoblastoid	RTeQTL
rs12459634	FLJ22573	cis	multi-tissue	Pritchard
rs12459634	U2AF1L4	cis	Whole Blood	GTEx
rs12459634	ENSG00000126246	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36210600-36230200	Strong transcription	HUES6 Cell Line	embryonic stem cell
2	chr19:36210600-36230200	Strong transcription	Cortex derived primary cultured neurospheres	brain
3	chr19:36210600-36230200	Strong transcription	Ovary	ovary
4	chr19:36210600-36230200	Strong transcription	Sigmoid Colon	Sigmoid Colon
5	chr19:36210600-36230400	Strong transcription	Brain Inferior Temporal Lobe	brain
6	chr19:36210600-36230400	Strong transcription	A549	lung
7	chr19:36210600-36230600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr19:36210600-36230600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr19:36210600-36230600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr19:36210600-36230600	Weak transcription	Right Atrium	heart
11	chr19:36210600-36230600	Strong transcription	NHLF	lung
12	chr19:36210600-36231200	Weak transcription	Fetal Brain Male	brain
13	chr19:36210800-36230200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr19:36210800-36230200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr19:36210800-36230200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr19:36210800-36230200	Strong transcription	Fetal Intestine Large	intestine
17	chr19:36210800-36230200	Strong transcription	Gastric	stomach
18	chr19:36210800-36230200	Strong transcription	Thymus	Thymus
19	chr19:36210800-36230400	Strong transcription	H9 Cell Line	embryonic stem cell
20	chr19:36210800-36230400	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr19:36210800-36230400	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr19:36210800-36230400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr19:36210800-36230400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr19:36210800-36230400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr19:36210800-36230400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr19:36210800-36230400	Strong transcription	Brain Cingulate Gyrus	brain
27	chr19:36210800-36230400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr19:36210800-36230400	Strong transcription	Colonic Mucosa	Colon
29	chr19:36210800-36230600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr19:36210800-36231000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr19:36211000-36230200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr19:36211000-36230200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr19:36211000-36230200	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr19:36211000-36230200	Strong transcription	Osteobl	bone
35	chr19:36211000-36230400	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr19:36211000-36230400	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr19:36211000-36230400	Strong transcription	Fetal Muscle Leg	muscle
38	chr19:36211000-36230400	Strong transcription	Lung	lung
39	chr19:36211000-36230600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
40	chr19:36211000-36230600	Strong transcription	Brain Germinal Matrix	brain
41	chr19:36211200-36230200	Strong transcription	Brain Anterior Caudate	brain
42	chr19:36211200-36230600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr19:36211200-36230600	Strong transcription	Fetal Intestine Small	intestine
44	chr19:36211200-36230600	Strong transcription	Fetal Stomach	stomach
45	chr19:36211400-36230200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr19:36211400-36230200	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr19:36211400-36230400	Strong transcription	Fetal Brain Female	brain
48	chr19:36211600-36230400	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr19:36211800-36230200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr19:36211800-36230200	Strong transcription	Duodenum Mucosa	Duodenum

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