Variant report

Variant	rs4465620
Chromosome Location	chr16:30432103-30432104
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:30431487-30432204	HL-60	blood:	n/a	n/a
2	POLR2A	chr16:30431923-30432233	GM12891	blood:	n/a	n/a
3	POLR2A	chr16:30431497-30432198	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr16:30431563-30432206	K562	blood:	n/a	n/a
5	POLR2A	chr16:30431484-30432430	GM12892	blood:	n/a	n/a
6	POLR2A	chr16:30431969-30432236	MCF-7	breast:	n/a	n/a
7	POLR2A	chr16:30431486-30432770	GM12892	blood:	n/a	n/a
8	POLR2A	chr16:30429888-30432822	HepG2	liver:	n/a	n/a
9	POLR2A	chr16:30432066-30432195	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr16:30431507-30432179	GM12892	blood:	n/a	n/a
11	POLR2A	chr16:30431364-30432586	PANC-1	pancreas:	n/a	n/a
12	POLR2A	chr16:30431554-30432323	K562	blood:	n/a	n/a
13	POLR2A	chr16:30431455-30432662	K562	blood:	n/a	n/a
14	POLR2A	chr16:30431865-30432192	K562	blood:	n/a	n/a
15	POLR2A	chr16:30431435-30432134	HepG2	liver:	n/a	n/a
16	PML	chr16:30431716-30432274	GM12878	blood:	n/a	n/a
17	POLR2A	chr16:30431440-30432746	GM12892	blood:	n/a	n/a
18	POLR2A	chr16:30431631-30432428	K562	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:30427757..30432109-chr16:30437396..30442167,10	MCF-7	breast:
2	chr16:30430091..30432882-chr16:30536696..30538204,2	K562	blood:
3	chr16:30364489..30367608-chr16:30429426..30432189,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000199787	TF binding region
ENSG00000260219	Chromatin interaction
ENSG00000179958	Chromatin interaction
ENSG00000169217	Chromatin interaction
ENSG00000169957	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11150586	0.88[CEU][hapmap];0.82[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[ASN][1000 genomes]
rs11640950	1.00[ASN][1000 genomes]
rs11646130	0.84[CEU][hapmap];0.82[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs11862806	0.84[CEU][hapmap];0.82[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap]
rs11863150	0.84[CEU][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap]
rs12446288	0.88[CEU][hapmap];0.82[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap]
rs12447833	0.80[EUR][1000 genomes]
rs12921440	0.88[CEU][hapmap];0.82[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs13333093	0.87[CEU][hapmap];0.82[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs35480350	0.84[CEU][hapmap];0.82[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs35598865	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3574	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4787642	0.84[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4787643	0.88[CEU][hapmap];0.82[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs4788409	0.88[CEU][hapmap];0.82[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs4788413	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs4788414	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62055459	0.81[EUR][1000 genomes]
rs6565182	0.84[CEU][hapmap];0.82[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs6565183	0.84[CEU][hapmap];0.82[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs7203359	0.84[CEU][hapmap];0.82[CHB][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs8045252	0.86[ASN][1000 genomes]
rs8045570	0.86[ASN][1000 genomes]
rs8046445	0.88[CEU][hapmap];0.82[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap]
rs8049108	0.84[CEU][hapmap];0.82[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap]
rs8050812	1.00[JPT][hapmap]
rs8051096	0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]
rs8060853	0.88[CEU][hapmap];0.82[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][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	nsv1065915	chr16:29967090-30486120	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	229 gene(s)	inside rSNPs	diseases
2	nsv542897	chr16:29967090-30486120	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	229 gene(s)	inside rSNPs	diseases
3	nsv1056897	chr16:30363683-30457504	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases
4	nsv905724	chr16:30368591-30438930	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
5	nsv532531	chr16:30370550-30581820	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	113 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4465620	TBX6	cis	parietal	SCAN
rs4465620	MAPK3	cis	parietal	SCAN
rs4465620	IMAA///LOC440345///LOC440354///LOC595101///	N/A	lymphoblastoid	RTeQTL
rs4465620	BOLA2///LOC440354///LOC595101	N/A	lymphoblastoid	RTeQTL
rs4465620	PPP4C	cis	cerebellum	SCAN
rs4465620	SEPHS2	cis	cerebellum	SCAN
rs4465620	GDPD3	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30421200-30437600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr16:30421200-30437600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr16:30428800-30440200	Weak transcription	Fetal Heart	heart
4	chr16:30429200-30435000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr16:30429600-30440200	Weak transcription	NHDF-Ad	bronchial
6	chr16:30429800-30432400	Weak transcription	Aorta	Aorta
7	chr16:30429800-30432800	Weak transcription	Lung	lung
8	chr16:30429800-30433200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr16:30429800-30433200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr16:30429800-30433400	Weak transcription	NHLF	lung
11	chr16:30429800-30433800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr16:30429800-30434800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr16:30429800-30434800	Weak transcription	Ovary	ovary
14	chr16:30429800-30435000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr16:30429800-30435400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr16:30429800-30440200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr16:30429800-30440200	Weak transcription	Fetal Kidney	kidney
18	chr16:30429800-30440200	Weak transcription	HSMMtube	muscle
19	chr16:30429800-30440400	Weak transcription	Right Atrium	heart
20	chr16:30430000-30432600	Weak transcription	Adipose Nuclei	Adipose
21	chr16:30430000-30433200	Weak transcription	Fetal Lung	lung
22	chr16:30430000-30433400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr16:30430000-30433400	Weak transcription	Primary hematopoietic stem cells	blood
24	chr16:30430000-30433400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr16:30430000-30433400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr16:30430000-30433400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr16:30430000-30433400	Weak transcription	Brain Germinal Matrix	brain
28	chr16:30430000-30433400	Weak transcription	Brain Hippocampus Middle	brain
29	chr16:30430000-30434000	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr16:30430000-30434800	Weak transcription	Brain Cingulate Gyrus	brain
31	chr16:30430000-30434800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr16:30430000-30435000	Weak transcription	Brain Angular Gyrus	brain
33	chr16:30430000-30435000	Weak transcription	NH-A	brain
34	chr16:30430000-30435200	Weak transcription	Rectal Smooth Muscle	rectum
35	chr16:30430000-30437200	Weak transcription	Brain Substantia Nigra	brain
36	chr16:30430000-30439400	Weak transcription	Fetal Brain Male	brain
37	chr16:30430000-30440200	Strong transcription	Fetal Intestine Small	intestine
38	chr16:30430000-30440400	Weak transcription	Small Intestine	intestine
39	chr16:30430000-30440600	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr16:30430200-30432200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr16:30430200-30432400	Weak transcription	Primary B cells from peripheral blood	blood
42	chr16:30430200-30432400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr16:30430200-30432800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr16:30430200-30433200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr16:30430200-30433400	Weak transcription	Primary B cells from cord blood	blood
46	chr16:30430200-30433400	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr16:30430200-30434000	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr16:30430200-30434800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr16:30430200-30434800	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr16:30430200-30434800	Weak transcription	Colonic Mucosa	Colon

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