Variant report

Variant	rs10519916
Chromosome Location	chr15:34533980-34533981
allele	C/T
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	RAD21	chr15:34533576-34533993	Hela-S3	cervix:	n/a	n/a
2	CTCF	chr15:34533599-34533984	MCF-7	breast:	n/a	chr15:34533758-34533779
3	RAD21	chr15:34533490-34533981	H1-hESC	embryonic stem cell:	n/a	n/a
4	RAD21	chr15:34533425-34534098	SK-N-SH	brain:	n/a	n/a
5	RAD21	chr15:34533591-34534081	A549	lung:	n/a	n/a
6	CTCF	chr15:34533217-34534104	SK-N-SH	brain:	n/a	chr15:34533758-34533779
7	RAD21	chr15:34533475-34534091	HCT-116	colon:	n/a	n/a
8	NFE2	chr15:34533877-34534033	GM12878	blood:	n/a	n/a
9	ARID3A	chr15:34533609-34534005	K562	blood:	n/a	n/a
10	RAD21	chr15:34533618-34534025	HCT-116	colon:	n/a	n/a
11	CTCF	chr15:34533554-34534008	HCT-116	colon:	n/a	chr15:34533758-34533779
12	CTCF	chr15:34532694-34534153	A549	lung:	n/a	chr15:34533758-34533779

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:34531119..34534573-chr15:34628473..34631118,3	MCF-7	breast:

Variant related genes	Relation type
SLC12A6	TF binding region
ENSG00000140199	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11544437	1.00[JPT][hapmap]
rs11630291	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs11638909	1.00[ASW][hapmap];0.81[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12438953	0.95[EUR][1000 genomes]
rs16958873	0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16958875	0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17236749	0.86[MEX][hapmap]
rs17236770	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17817770	0.86[MEX][hapmap]
rs3764236	0.86[MEX][hapmap]
rs3794517	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs4779660	1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7161944	0.86[MEX][hapmap]
rs7177365	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs73386041	0.96[EUR][1000 genomes]
rs74010034	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74010036	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74010045	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs74010046	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs74010057	0.81[AMR][1000 genomes]
rs74010058	0.81[AMR][1000 genomes]
rs8028501	0.81[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs8033087	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8039731	1.00[YRI][hapmap]
rs8043447	0.85[YRI][hapmap]
rs991076	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052804	chr15:34498529-34841447	Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv542341	chr15:34498529-34841447	Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1045173	chr15:34501055-34596995	Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10519916	HERC2	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:34518000-34571800	Weak transcription	Stomach Mucosa	stomach
2	chr15:34518800-34548200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr15:34519000-34552400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr15:34519200-34534000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr15:34519200-34552200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr15:34519200-34553600	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr15:34519400-34540800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr15:34519400-34552200	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr15:34519400-34552200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr15:34519600-34538400	Strong transcription	Fetal Intestine Large	intestine
11	chr15:34519600-34544200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr15:34519600-34553600	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr15:34519800-34540000	Strong transcription	Liver	Liver
14	chr15:34519800-34544800	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr15:34520200-34555600	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr15:34521000-34547800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr15:34523000-34535800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:34523000-34545600	Weak transcription	Dnd41	blood
19	chr15:34524200-34538200	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr15:34524200-34552400	Strong transcription	Primary B cells from cord blood	blood
21	chr15:34524400-34538000	Strong transcription	Skeletal Muscle Female	skeletal muscle
22	chr15:34524800-34553600	Strong transcription	Primary B cells from peripheral blood	blood
23	chr15:34525200-34540400	Strong transcription	Primary T cells from cord blood	blood
24	chr15:34526200-34537000	Weak transcription	HepG2	liver
25	chr15:34528400-34535600	Weak transcription	Fetal Brain Male	brain
26	chr15:34528400-34546400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr15:34528400-34547400	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr15:34528600-34554600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr15:34529000-34537400	Weak transcription	Fetal Intestine Small	intestine
30	chr15:34529000-34543800	Weak transcription	Right Ventricle	heart
31	chr15:34529000-34554800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr15:34529200-34542800	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr15:34529200-34544000	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr15:34529200-34546000	Weak transcription	Gastric	stomach
35	chr15:34529200-34550400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr15:34529200-34552200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr15:34529800-34537600	Weak transcription	Colonic Mucosa	Colon
38	chr15:34529800-34542600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr15:34529800-34544000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr15:34529800-34546200	Weak transcription	Esophagus	oesophagus
41	chr15:34530800-34541600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr15:34531400-34537400	Weak transcription	Lung	lung
43	chr15:34531400-34540800	Weak transcription	Psoas Muscle	Psoas
44	chr15:34531400-34541000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr15:34531400-34542200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr15:34531400-34546000	Weak transcription	Spleen	Spleen
47	chr15:34531400-34546400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr15:34531800-34537000	Weak transcription	Aorta	Aorta
49	chr15:34532000-34534000	Enhancers	NHEK	skin
50	chr15:34532000-34535400	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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