Variant report

Variant	rs16903460
Chromosome Location	chr5:14394556-14394557
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:14394554-14394636	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr5:14394469-14394921	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr5:14394292-14394845	U87	brain:	n/a	n/a
4	POLR2A	chr5:14394292-14394941	U87	brain:	n/a	n/a
5	POLR2A	chr5:14394376-14394837	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:14393059..14395899-chr5:14399297..14401999,2	K562	blood:

Variant related genes	Relation type
TRIO	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10866506	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10866507	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11949756	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11950000	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs11959397	0.89[EUR][1000 genomes]
rs12109453	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12109756	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12109880	0.89[EUR][1000 genomes]
rs12110161	1.00[CEU][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12110267	0.89[EUR][1000 genomes]
rs16903421	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs16903423	0.89[EUR][1000 genomes]
rs16903428	0.89[EUR][1000 genomes]
rs16903434	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16903453	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16903464	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16903497	1.00[YRI][hapmap]
rs2463803	0.85[CEU][hapmap]
rs35373258	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56689214	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57017859	0.89[EUR][1000 genomes]
rs57640930	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59405120	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60738268	0.89[EUR][1000 genomes]
rs60892841	0.93[EUR][1000 genomes]
rs61059406	0.89[EUR][1000 genomes]
rs61469842	0.84[EUR][1000 genomes]
rs62344979	0.89[EUR][1000 genomes]
rs62344981	0.86[EUR][1000 genomes]
rs62344983	0.89[EUR][1000 genomes]
rs62345009	0.84[EUR][1000 genomes]
rs62345012	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62345015	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66554336	0.89[EUR][1000 genomes]
rs6883134	1.00[YRI][hapmap]
rs697559	0.82[CEU][hapmap]
rs73061636	0.91[EUR][1000 genomes]
rs7706484	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7715916	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs773764	0.82[CEU][hapmap]
rs773765	0.82[CEU][hapmap]
rs773766	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948355	chr5:14160447-14395478	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv1026914	chr5:14237782-14751588	Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv830210	chr5:14255039-14431552	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1018187	chr5:14385164-15127103	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14351600-14399400	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr5:14353600-14398800	Strong transcription	Rectal Mucosa Donor 29	rectum
3	chr5:14354600-14402400	Strong transcription	Liver	Liver
4	chr5:14355000-14398800	Strong transcription	Rectal Mucosa Donor 31	rectum
5	chr5:14357600-14422000	Weak transcription	Stomach Mucosa	stomach
6	chr5:14360000-14398400	Strong transcription	Fetal Muscle Trunk	muscle
7	chr5:14363600-14396000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr5:14363800-14430600	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr5:14363800-14430600	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr5:14366800-14403200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr5:14367400-14399800	Strong transcription	Left Ventricle	heart
12	chr5:14372400-14398600	Strong transcription	Sigmoid Colon	Sigmoid Colon
13	chr5:14374400-14397000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr5:14374400-14399600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr5:14375800-14396200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr5:14377000-14396200	Strong transcription	Muscle Satellite Cultured Cells	--
17	chr5:14380400-14402800	Strong transcription	Primary B cells from peripheral blood	blood
18	chr5:14380800-14396200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr5:14383600-14396800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr5:14385600-14399000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr5:14386400-14399600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr5:14386800-14398600	Strong transcription	Skeletal Muscle Female	skeletal muscle
23	chr5:14387000-14396000	Strong transcription	Hela-S3	cervix
24	chr5:14387200-14397800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr5:14387200-14398600	Strong transcription	A549	lung
26	chr5:14387200-14405800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr5:14387600-14396400	Strong transcription	Osteobl	bone
28	chr5:14387800-14396800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr5:14387800-14396800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr5:14387800-14399800	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr5:14388000-14397200	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr5:14388000-14399600	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr5:14388000-14402200	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr5:14388200-14397000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr5:14388200-14398000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr5:14388200-14400200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr5:14388400-14397200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr5:14388600-14394600	Weak transcription	Thymus	Thymus
39	chr5:14388600-14395600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr5:14388600-14398000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr5:14388600-14399600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr5:14388600-14402600	Strong transcription	Fetal Intestine Large	intestine
43	chr5:14388800-14407200	Weak transcription	Small Intestine	intestine
44	chr5:14389000-14398000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr5:14389600-14396000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr5:14390200-14397400	Strong transcription	Adipose Nuclei	Adipose
47	chr5:14390600-14399800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr5:14391000-14397200	Weak transcription	Gastric	stomach
49	chr5:14392000-14395600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr5:14392000-14397000	Weak transcription	Spleen	Spleen

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