Variant report

Variant	rs11670437
Chromosome Location	chr19:18783390-18783391
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:18699407..18701791-chr19:18783054..18785854,2	K562	blood:
2	chr19:18781923..18783867-chr19:18787837..18789720,2	K562	blood:
3	chr19:18704952..18705456-chr19:18783349..18784188,2	MCF-7	breast:
4	chr19:18781390..18783867-chr19:18783988..18789720,5	K562	blood:
5	chr19:18781801..18783943-chr19:18794060..18796005,2	MCF-7	breast:
6	chr19:18758073..18760878-chr19:18781482..18783635,2	K562	blood:
7	chr19:18777346..18780896-chr19:18782148..18785214,5	K562	blood:

Variant related genes	Relation type
ENSG00000006016	Chromatin interaction
ENSG00000006015	Chromatin interaction
ENSG00000105662	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11665980	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11667450	0.83[ASN][1000 genomes]
rs11668413	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11672177	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12972147	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12973480	0.85[CEU][hapmap];1.00[GIH][hapmap]
rs17683569	1.00[CHB][hapmap]
rs17683623	0.85[CEU][hapmap]
rs2238649	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs35322184	0.93[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3752217	0.91[CEU][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3752218	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3764628	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3795027	0.88[CHD][hapmap]
rs61248595	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66840797	0.97[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs66969630	0.97[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs68074367	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72997346	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72997355	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs752981	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8107912	1.00[CHB][hapmap]
rs8108207	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv532615	chr19:18534867-18796031	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	nsv911282	chr19:18624964-18928480	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv911286	chr19:18652844-18811112	Active TSS Flanking Active TSS Enhancers Strong transcription 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 miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv911289	chr19:18700047-18811112	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11670437	CYP4F12	cis	cerebellum	SCAN
rs11670437	TSSK6	cis	parietal	SCAN
rs11670437	TMEM59L	cis	cerebellum	SCAN
rs11670437	CRLF1	cis	parietal	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18760400-18794800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr19:18770400-18793600	Weak transcription	GM12878-XiMat	blood
3	chr19:18771600-18783400	Weak transcription	HUVEC	blood vessel
4	chr19:18771800-18788200	Weak transcription	K562	blood
5	chr19:18773200-18788000	Weak transcription	NHEK	skin
6	chr19:18774200-18783400	Weak transcription	A549	lung
7	chr19:18774400-18784000	Strong transcription	Fetal Intestine Small	intestine
8	chr19:18774600-18783800	Weak transcription	HepG2	liver
9	chr19:18774600-18787400	Weak transcription	Hela-S3	cervix
10	chr19:18774800-18788000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr19:18775200-18793800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr19:18775600-18783400	Strong transcription	Dnd41	blood
13	chr19:18776000-18783600	Strong transcription	Thymus	Thymus
14	chr19:18776200-18783400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr19:18777800-18793800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr19:18778400-18783400	Strong transcription	Primary T cells from cord blood	blood
17	chr19:18779800-18783400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr19:18780000-18785000	Weak transcription	Brain Angular Gyrus	brain
19	chr19:18780000-18788200	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr19:18780000-18788800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr19:18780200-18784000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr19:18780200-18786800	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr19:18780200-18788000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr19:18780200-18788000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr19:18780200-18788800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr19:18780200-18793400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr19:18780200-18793800	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr19:18780400-18783400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr19:18780400-18788000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr19:18780400-18788000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr19:18780400-18793800	Weak transcription	Right Ventricle	heart
32	chr19:18780600-18784800	Weak transcription	Brain Anterior Caudate	brain
33	chr19:18780600-18788000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr19:18780600-18788200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr19:18780600-18788800	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr19:18780800-18784200	Weak transcription	Colonic Mucosa	Colon
37	chr19:18780800-18784600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr19:18780800-18785400	Weak transcription	Duodenum Mucosa	Duodenum
39	chr19:18780800-18793800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr19:18780800-18793800	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr19:18781000-18783400	Weak transcription	NH-A	brain
42	chr19:18781000-18784800	Weak transcription	Aorta	Aorta
43	chr19:18781000-18785400	Weak transcription	Left Ventricle	heart
44	chr19:18781000-18785400	Weak transcription	Ovary	ovary
45	chr19:18781000-18785600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr19:18781000-18787200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr19:18781000-18788000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr19:18781000-18789000	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr19:18781000-18793800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr19:18781200-18785200	Weak transcription	Primary T helper cells fromperipheralblood	blood

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