Variant report

Variant	rs13384575
Chromosome Location	chr2:234759743-234759744
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:234755154-234760215	U87	brain:	n/a	n/a
2	POLR2A	chr2:234755022-234759760	K562	blood:	n/a	n/a
3	POLR2A	chr2:234757697-234759829	HepG2	liver:	n/a	n/a
4	POLR2A	chr2:234745990-234762655	K562	blood:	n/a	n/a
5	POLR2A	chr2:234754982-234760241	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr2:234759442-234760048	K562	blood:	n/a	n/a
7	POLR2A	chr2:234757285-234759804	GM12878	blood:	n/a	n/a
8	POLR2A	chr2:234755017-234760215	U87	brain:	n/a	n/a
9	POLR2A	chr2:234758416-234759794	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr2:234758197..234760837-chr2:234836027..234838488,2	K562	blood:
2	chr2:234753471..234756128-chr2:234758714..234761959,3	MCF-7	breast:
3	chr2:234747927..234752617-chr2:234757241..234760452,5	MCF-7	breast:

No data

Variant related genes	Relation type
HJURP	TF binding region
ENSG00000144481	Chromatin interaction
ENSG00000123485	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10173569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11562979	0.94[EUR][1000 genomes]
rs11563228	0.94[EUR][1000 genomes]
rs11563231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13384669	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13390819	0.94[EUR][1000 genomes]
rs13398248	0.84[EUR][1000 genomes]
rs13403318	0.94[EUR][1000 genomes]
rs13406453	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs13406457	0.84[EUR][1000 genomes]
rs13410024	0.94[EUR][1000 genomes]
rs13410032	0.94[EUR][1000 genomes]
rs13417465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13427471	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17862903	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17862907	0.94[EUR][1000 genomes]
rs17863825	0.94[EUR][1000 genomes]
rs17863826	0.94[EUR][1000 genomes]
rs17864729	0.94[EUR][1000 genomes]
rs17868368	0.94[EUR][1000 genomes]
rs17868369	0.88[EUR][1000 genomes]
rs213556	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2173746	0.94[EUR][1000 genomes]
rs2173747	0.94[EUR][1000 genomes]
rs2530796	0.94[EUR][1000 genomes]
rs2650888	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs3771333	0.85[CHD][hapmap]
rs473504	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs494812	0.94[EUR][1000 genomes]
rs498680	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs498696	0.94[EUR][1000 genomes]
rs498786	0.88[EUR][1000 genomes]
rs498790	0.88[EUR][1000 genomes]
rs499703	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs501650	0.94[EUR][1000 genomes]
rs502321	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs506632	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs522389	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs529963	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs531771	0.94[EUR][1000 genomes]
rs536265	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs566529	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs575194	0.94[EUR][1000 genomes]
rs577734	0.94[EUR][1000 genomes]
rs577782	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs577820	0.94[EUR][1000 genomes]
rs579327	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs581377	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs596509	0.94[EUR][1000 genomes]
rs598759	0.87[EUR][1000 genomes]
rs598760	0.88[EUR][1000 genomes]
rs606397	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs611131	0.94[EUR][1000 genomes]
rs611169	0.94[EUR][1000 genomes]
rs611563	0.94[EUR][1000 genomes]
rs619351	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs625151	0.94[EUR][1000 genomes]
rs628138	0.94[EUR][1000 genomes]
rs657658	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs658054	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs658607	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs672831	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs686003	0.94[EUR][1000 genomes]
rs686007	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs686802	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs688677	0.94[EUR][1000 genomes]
rs693637	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv876023	chr2:234726154-234763137	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13384575	PDE6D	cis	parietal	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234736400-234762600	Weak transcription	Right Atrium	heart
2	chr2:234738200-234762000	Weak transcription	Esophagus	oesophagus
3	chr2:234740000-234760000	Strong transcription	Thymus	Thymus
4	chr2:234740200-234761000	Weak transcription	Primary B cells from cord blood	blood
5	chr2:234740400-234762200	Weak transcription	Primary T cells from cord blood	blood
6	chr2:234741200-234759800	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr2:234741800-234762000	Weak transcription	Gastric	stomach
8	chr2:234742200-234760400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:234742200-234762200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr2:234742600-234759800	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr2:234742600-234760400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:234742600-234760600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr2:234742600-234760600	Strong transcription	NHEK	skin
14	chr2:234742600-234760800	Strong transcription	H9 Cell Line	embryonic stem cell
15	chr2:234742800-234759800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr2:234742800-234760400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr2:234742800-234760600	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr2:234742800-234760600	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr2:234742800-234760800	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr2:234743000-234760000	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr2:234743000-234760000	Strong transcription	HMEC	breast
22	chr2:234743000-234760800	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr2:234743000-234760800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr2:234743000-234761200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr2:234743200-234760200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr2:234743200-234760600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr2:234743200-234760600	Strong transcription	Fetal Muscle Leg	muscle
28	chr2:234743800-234759800	Strong transcription	Osteobl	bone
29	chr2:234744000-234760400	Strong transcription	K562	blood
30	chr2:234744000-234762400	Weak transcription	Small Intestine	intestine
31	chr2:234744600-234762000	Weak transcription	Colonic Mucosa	Colon
32	chr2:234747800-234760400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr2:234748000-234760400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
34	chr2:234748000-234760400	Strong transcription	Fetal Stomach	stomach
35	chr2:234748200-234760600	Strong transcription	Fetal Muscle Trunk	muscle
36	chr2:234748400-234760600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr2:234748600-234762000	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr2:234749200-234759800	Strong transcription	HepG2	liver
39	chr2:234749200-234760400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr2:234749200-234760400	Strong transcription	Hela-S3	cervix
41	chr2:234749200-234761600	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr2:234749400-234760600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr2:234750600-234761400	Weak transcription	Fetal Brain Female	brain
44	chr2:234751200-234760800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr2:234752800-234761600	Weak transcription	Fetal Kidney	kidney
46	chr2:234753200-234760600	Weak transcription	Spleen	Spleen
47	chr2:234753200-234761600	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr2:234753200-234762200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr2:234753600-234760600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr2:234753800-234760400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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