Variant report

Variant	rs6573788
Chromosome Location	chr14:68089823-68089824
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:68084874..68087347-chr14:68088536..68091014,3	MCF-7	breast:
2	chr14:68087492..68090033-chr14:68140902..68143299,2	K562	blood:
3	chr14:68087429..68090959-chr14:68140902..68143927,4	K562	blood:
4	chr14:68073077..68076511-chr14:68087971..68090364,3	K562	blood:

Variant related genes	Relation type
ENSG00000081181	Chromatin interaction
ENSG00000100568	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10483801	0.80[CHB][hapmap];0.82[CHD][hapmap]
rs11628590	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11628666	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12433361	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13343243	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17249437	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17249444	0.89[MEX][hapmap];0.81[MKK][hapmap]
rs17836809	0.95[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap]
rs1885042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3742878	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3759757	0.94[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3759759	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4902501	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902503	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6573787	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66517376	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67778250	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7144243	0.84[CEU][hapmap];0.81[TSI][hapmap]
rs7151920	0.95[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7161243	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8012815	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8013117	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8014035	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8014048	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456331	chr14:67732861-68103780	Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv564961	chr14:67732861-68103780	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv470651	chr14:67732861-68113293	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv902066	chr14:67873128-68103780	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv902068	chr14:68083133-68204876	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6573788	RDH11	Cis_1M	lymphoblastoid	RTeQTL
rs6573788	RDH11	cis	Nerve Tibial	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:68087200-68109600	Weak transcription	Gastric	stomach
2	chr14:68087200-68112400	Weak transcription	Aorta	Aorta
3	chr14:68087600-68091600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr14:68087600-68097400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr14:68087800-68090800	Enhancers	HepG2	liver
6	chr14:68087800-68112000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr14:68088000-68091600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr14:68088000-68100000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr14:68088000-68112400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr14:68088000-68112400	Weak transcription	Brain Angular Gyrus	brain
11	chr14:68088000-68112600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr14:68088200-68097600	Weak transcription	Brain Germinal Matrix	brain
13	chr14:68088600-68090000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr14:68088600-68090200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr14:68088800-68090000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr14:68088800-68090000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr14:68088800-68090200	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr14:68088800-68090200	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr14:68088800-68090800	Enhancers	Primary T cells from cord blood	blood
20	chr14:68088800-68091000	Enhancers	Hela-S3	cervix
21	chr14:68088800-68123000	Weak transcription	Fetal Brain Male	brain
22	chr14:68089000-68090000	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr14:68089000-68090000	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr14:68089000-68090000	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr14:68089000-68090000	Enhancers	Rectal Smooth Muscle	rectum
26	chr14:68089000-68090200	Enhancers	H1 Cell Line	embryonic stem cell
27	chr14:68089000-68090200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr14:68089000-68090200	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr14:68089000-68090200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr14:68089000-68090200	Enhancers	Muscle Satellite Cultured Cells	--
31	chr14:68089000-68090200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr14:68089000-68090200	Enhancers	Brain Anterior Caudate	brain
33	chr14:68089000-68090200	Enhancers	Colon Smooth Muscle	Colon
34	chr14:68089000-68090400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr14:68089000-68090600	Enhancers	HMEC	breast
36	chr14:68089000-68090800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr14:68089000-68090800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr14:68089000-68090800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr14:68089200-68090000	Enhancers	HSMMtube	muscle
40	chr14:68089200-68090000	Flanking Active TSS	HUVEC	blood vessel
41	chr14:68089200-68090200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
42	chr14:68089200-68090200	Enhancers	Primary hematopoietic stem cells	blood
43	chr14:68089200-68090200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr14:68089200-68090200	Enhancers	Adipose Nuclei	Adipose
45	chr14:68089200-68090200	Enhancers	Fetal Heart	heart
46	chr14:68089200-68090200	Enhancers	NH-A	brain
47	chr14:68089200-68090200	Enhancers	NHLF	lung
48	chr14:68089200-68090200	Enhancers	Osteobl	bone
49	chr14:68089200-68090400	Weak transcription	Psoas Muscle	Psoas
50	chr14:68089200-68090800	Enhancers	Primary T helper cells PMA-I stimulated	--

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