Variant report

Variant	rs11729
Chromosome Location	chr19:19230482-19230483
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19229446..19234006-chr19:19241302..19251526,15	K562	blood:
2	chr19:19229745..19232931-chr19:19245473..19249545,7	K562	blood:
3	chr19:19228835..19230713-chr19:19234651..19236877,2	K562	blood:
4	chr19:19169419..19177029-chr19:19229685..19233171,13	K562	blood:
5	chr19:19215063..19218544-chr19:19229817..19231578,4	K562	blood:
6	chr19:19216749..19218544-chr19:19229927..19231578,2	K562	blood:
7	chr19:19142905..19145164-chr19:19230033..19232752,3	K562	blood:
8	chr19:19170341..19177029-chr19:19229928..19235464,11	K562	blood:

No data

Variant related genes	Relation type
ENSG00000105676	Chromatin interaction
ENSG00000181035	Chromatin interaction
ENSG00000064545	Chromatin interaction
ENSG00000064607	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1004079	1.00[JPT][hapmap]
rs1007483	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs10221504	0.84[EUR][1000 genomes]
rs10405635	0.84[EUR][1000 genomes]
rs10410223	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10410451	0.86[CEU][hapmap]
rs10415987	0.85[EUR][1000 genomes]
rs10417974	0.82[GIH][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs10421019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10422906	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10423742	0.87[CEU][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs11666627	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs12979841	0.81[EUR][1000 genomes]
rs12985799	0.86[CEU][hapmap];0.80[GIH][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs16994664	1.00[JPT][hapmap]
rs16995852	1.00[JPT][hapmap]
rs2012318	0.86[CEU][hapmap];0.80[GIH][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs2269806	0.86[CEU][hapmap];0.80[GIH][hapmap];0.91[TSI][hapmap]
rs2285851	0.80[CEU][hapmap];0.91[TSI][hapmap]
rs4808916	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs4808923	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6511018	0.86[CEU][hapmap];0.80[GIH][hapmap];0.91[TSI][hapmap]
rs6511019	0.91[MEX][hapmap]
rs7248399	0.86[CEU][hapmap];0.80[GIH][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs7250131	0.80[EUR][1000 genomes]
rs7256648	0.86[CEU][hapmap]
rs7259609	0.86[CEU][hapmap];0.80[GIH][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs756791	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs756792	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs757220	0.86[CEU][hapmap];0.80[GIH][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs757221	0.81[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833779	chr19:19163492-19313091	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11729	ZNF14	cis	parietal	SCAN
rs11729	SLC25A42	cis	lung	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19180600-19245600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr19:19180600-19248400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr19:19203800-19245600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr19:19212600-19240800	Weak transcription	Aorta	Aorta
5	chr19:19217000-19236800	Weak transcription	Hela-S3	cervix
6	chr19:19217200-19247800	Weak transcription	Right Atrium	heart
7	chr19:19220400-19247800	Weak transcription	Psoas Muscle	Psoas
8	chr19:19220800-19242800	Weak transcription	Osteobl	bone
9	chr19:19221400-19232600	Weak transcription	HSMMtube	muscle
10	chr19:19221800-19231400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr19:19221800-19235200	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr19:19221800-19242800	Weak transcription	Spleen	Spleen
13	chr19:19221800-19243200	Weak transcription	A549	lung
14	chr19:19222000-19230600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr19:19222000-19240800	Weak transcription	Primary hematopoietic stem cells	blood
16	chr19:19222200-19231400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr19:19222200-19233600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr19:19222200-19248200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr19:19222400-19230800	Weak transcription	Placenta	Placenta
20	chr19:19223200-19233400	Weak transcription	GM12878-XiMat	blood
21	chr19:19224000-19233600	Weak transcription	Fetal Lung	lung
22	chr19:19224200-19231600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr19:19224400-19233800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr19:19224400-19233800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr19:19224400-19234000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr19:19226200-19230800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr19:19226600-19231800	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr19:19226800-19233000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr19:19226800-19242600	Weak transcription	HepG2	liver
30	chr19:19227000-19230600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr19:19227000-19239800	Weak transcription	Fetal Kidney	kidney
32	chr19:19228000-19232600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr19:19229200-19230800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr19:19229200-19232600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr19:19229200-19232800	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr19:19229200-19234000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr19:19229400-19230600	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr19:19229400-19230600	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr19:19229400-19230800	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr19:19229400-19230800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
41	chr19:19229400-19230800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr19:19229400-19230800	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr19:19229400-19230800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr19:19229400-19230800	Strong transcription	Fetal Brain Female	brain
45	chr19:19229400-19231000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr19:19229400-19231000	Strong transcription	Fetal Thymus	thymus
47	chr19:19229400-19231200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr19:19229400-19231400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr19:19229400-19231400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr19:19229400-19231600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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