Variant report

Variant	rs1236716
Chromosome Location	chr19:44640929-44640930
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:44635509..44637691-chr19:44639057..44641237,2	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10406335	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs10408901	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.94[ASN][1000 genomes]
rs10410306	0.82[CHB][hapmap]
rs10413195	0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.97[ASN][1000 genomes]
rs10413511	0.88[ASN][1000 genomes]
rs10853771	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1236712	0.93[ASN][1000 genomes]
rs1236715	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12608984	0.82[JPT][hapmap]
rs2061332	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2061333	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs2168778	0.95[ASN][1000 genomes]
rs2284980	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs2284981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2356750	0.95[ASN][1000 genomes]
rs3172	0.87[CEU][hapmap];0.81[CHB][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3200505	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3746319	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3746321	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4239529	0.83[CHB][hapmap]
rs4429390	0.83[CHB][hapmap];0.88[TSI][hapmap]
rs4459653	0.83[CHB][hapmap];0.83[GIH][hapmap];0.88[TSI][hapmap]
rs4508518	1.00[CEU][hapmap];0.86[CHB][hapmap];0.80[GIH][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs4802206	0.81[CHB][hapmap]
rs4802207	0.88[CEU][hapmap];0.81[CHB][hapmap];0.80[GIH][hapmap];0.92[TSI][hapmap]
rs4802208	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4803676	0.83[CHB][hapmap]
rs4803681	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs7251868	0.94[ASN][1000 genomes]
rs7253485	0.88[AFR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7508149	0.86[CHB][hapmap]
rs7508762	0.95[ASN][1000 genomes]
rs8099869	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8104573	0.82[CHB][hapmap]
rs8105860	0.82[CHB][hapmap]
rs8108021	0.88[CEU][hapmap]
rs9304638	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][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	nsv833840	chr19:44520620-44715760	Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1236716	ZNF221	cis	multi-tissue	Pritchard
rs1236716	KLK10	cis	cerebellum	SCAN
rs1236716	SIGLEC12	cis	parietal	SCAN
rs1236716	SNORD34	cis	parietal	SCAN
rs1236716	FUT2	cis	parietal	SCAN
rs1236716	CLPTM1	cis	cerebellum	SCAN
rs1236716	APOE	cis	parietal	SCAN
rs1236716	SNRPD2	cis	cerebellum	SCAN
rs1236716	ZNF221	cis	Lymphoblastoid	GTEx
rs1236716	ZNF224	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44622800-44645000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr19:44630600-44645000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:44635800-44645000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr19:44636000-44644800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr19:44636000-44645000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr19:44636000-44645000	Weak transcription	Brain Angular Gyrus	brain
7	chr19:44636000-44645200	Weak transcription	Fetal Thymus	thymus
8	chr19:44636200-44643600	Weak transcription	Fetal Heart	heart
9	chr19:44636200-44645000	Weak transcription	NHDF-Ad	bronchial
10	chr19:44636600-44644600	Weak transcription	Right Ventricle	heart
11	chr19:44636600-44645000	Weak transcription	Fetal Intestine Large	intestine
12	chr19:44636600-44645000	Weak transcription	Placenta	Placenta
13	chr19:44636800-44644000	Weak transcription	Brain Germinal Matrix	brain
14	chr19:44636800-44644000	Weak transcription	Left Ventricle	heart
15	chr19:44636800-44644000	Weak transcription	Pancreas	Pancrea
16	chr19:44636800-44644000	Weak transcription	Dnd41	blood
17	chr19:44636800-44644800	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr19:44636800-44644800	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr19:44636800-44644800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr19:44636800-44644800	Weak transcription	Brain Anterior Caudate	brain
21	chr19:44636800-44644800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr19:44636800-44645000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr19:44636800-44645000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr19:44636800-44645000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr19:44636800-44645200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr19:44637000-44645000	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr19:44637000-44645000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr19:44637000-44645000	Weak transcription	NH-A	brain
29	chr19:44637200-44644000	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr19:44637200-44644200	Weak transcription	Fetal Brain Male	brain
31	chr19:44637200-44644600	Weak transcription	Fetal Muscle Trunk	muscle
32	chr19:44637200-44644800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr19:44637200-44644800	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr19:44637200-44645000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr19:44637200-44645000	Weak transcription	HSMM	muscle
36	chr19:44637400-44643200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr19:44637400-44644200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr19:44637400-44644600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr19:44637400-44644800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr19:44637400-44644800	Weak transcription	Fetal Kidney	kidney
41	chr19:44637400-44645000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr19:44637600-44644800	Weak transcription	Primary B cells from cord blood	blood
43	chr19:44637600-44644800	Weak transcription	Fetal Brain Female	brain
44	chr19:44637600-44645000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr19:44637800-44645000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr19:44638600-44643600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr19:44638800-44644800	Weak transcription	Fetal Lung	lung
48	chr19:44639200-44644800	Weak transcription	Psoas Muscle	Psoas
49	chr19:44640400-44644000	Weak transcription	Skeletal Muscle Male	skeletal muscle

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