Variant report

Variant	rs2708875
Chromosome Location	chr7:47990681-47990682
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:28)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:28 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr7:47990332-47990697	T-47D	breast:	n/a	n/a
2	RAD21	chr7:47990305-47990730	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr7:47990476-47990720	H1-hESC	embryonic stem cell:	n/a	chr7:47990544-47990553
4	CTCF	chr7:47990536-47990686	MCF-7	breast:	n/a	chr7:47990544-47990553
5	GATA3	chr7:47990171-47991966	MCF-7	breast:	n/a	chr7:47991804-47991820 chr7:47991802-47991823 chr7:47991701-47991710 chr7:47991804-47991820
6	ZNF263	chr7:47990386-47990705	HEK293-T-REx	kidney:	n/a	n/a
7	GATA3	chr7:47990230-47990701	T-47D	breast:	n/a	n/a
8	CTCF	chr7:47990540-47990690	HEEpiC	esophagus:	n/a	chr7:47990544-47990553
9	CTCF	chr7:47990539-47990683	MCF-7	breast:	n/a	chr7:47990544-47990553
10	FOXA2	chr7:47990660-47991584	HepG2	liver:	n/a	n/a
11	CTCF	chr7:47990489-47990692	H1-hESC	embryonic stem cell:	n/a	chr7:47990544-47990553
12	CTCF	chr7:47990476-47990706	MCF-7	breast:	n/a	chr7:47990544-47990553
13	IRF1	chr7:47990553-47990696	K562	blood:	n/a	n/a
14	CTCF	chr7:47990580-47990730	MCF-7	breast:	n/a	n/a
15	CTCF	chr7:47990540-47990690	HPAF	blood vessel:	n/a	chr7:47990544-47990553
16	CTCF	chr7:47990540-47990690	Caco-2	colon:	n/a	chr7:47990544-47990553
17	TEAD4	chr7:47990359-47990713	H1-hESC	embryonic stem cell:	n/a	n/a
18	CTCF	chr7:47990531-47990689	K562	blood:	n/a	chr7:47990544-47990553
19	CTCF	chr7:47990571-47990690	HUVEC	blood vessel:	n/a	n/a
20	RAD21	chr7:47990433-47990733	H1-hESC	embryonic stem cell:	n/a	n/a
21	TCF12	chr7:47990376-47990708	H1-hESC	embryonic stem cell:	n/a	n/a
22	GATA3	chr7:47990260-47990684	T-47D	breast:	n/a	n/a
23	TEAD4	chr7:47990322-47990725	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr7:47990369-47990736	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr7:47990231-47990792	HUVEC	blood vessel:	n/a	n/a
26	RAD21	chr7:47990413-47990692	H1-hESC	embryonic stem cell:	n/a	n/a
27	CTCF	chr7:47990540-47990690	HUVEC	blood vessel:	n/a	chr7:47990544-47990553
28	ZNF143	chr7:47990439-47990717	H1-hESC	embryonic stem cell:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:47990680-47990730	HMEC	breast:	n/a
2	chr7:47990680-47990730	Caco-2	colon:	n/a
3	chr7:47990680-47990730	ProgFib	skin:	n/a
4	chr7:47990680-47990730	GM12891	blood:	n/a
5	chr7:47990680-47990730	RPTEC	kidney:	n/a
6	chr7:47990680-47990730	ECC-1	luminal epithelium:	n/a
7	chr7:47990680-47990730	AoSMC	blood vessel:	n/a
8	chr7:47990680-47990730	HRE	kidney:	n/a
9	chr7:47990680-47990730	HPAEpiC	pulmonary alveolar:	n/a
10	chr7:47990680-47990730	Hepatocyte	liver:	n/a
11	chr7:47990680-47990730	SK-N-SH_RA	brain:	n/a
12	chr7:47990680-47990730	GM12892	blood:	n/a
13	chr7:47990680-47990730	CMK	blood:	n/a
14	chr7:47990680-47990730	SKMC	muscle:	n/a
15	chr7:47990680-47990730	SK-N-MC	brain:	n/a
16	chr7:47990680-47990730	K562	blood:	n/a
17	chr7:47990680-47990730	HCF	heart:	n/a
18	chr7:47990680-47990730	PANC-1	pancreas:	n/a
19	chr7:47990680-47990730	HEK293	kidney:	embryo
20	chr7:47990680-47990730	SAEC	small airway:	n/a
21	chr7:47990680-47990730	NB4	blood:	n/a
22	chr7:47990680-47990730	NT2-D1	testis:	n/a
23	chr7:47990680-47990730	HRPEpiC	eye:	n/a
24	chr7:47990680-47990730	AG09309	skin:	n/a
25	chr7:47990680-47990730	GM06990	blood:	n/a
26	chr7:47990680-47990730	AG04449	skin:	fetal
27	chr7:47990680-47990730	GM19239	blood:	n/a
28	chr7:47990680-47990730	U87	brain:	n/a
29	chr7:47990680-47990730	Hela-S3	cervix:	n/a
30	chr7:47990680-47990730	PrEC	prostate:	n/a
31	chr7:47990680-47990730	HCM	heart:	n/a
32	chr7:47990680-47990730	MCF10A-Er-Src	breast:	n/a
33	chr7:47990680-47990730	NH-A	brain:	n/a
34	chr7:47990680-47990730	A549	lung:	n/a
35	chr7:47990680-47990730	GM12878	blood:	n/a
36	chr7:47990680-47990730	Jurkat	blood:	n/a
37	chr7:47990680-47990730	PFSK-1	brain:	n/a
38	chr7:47990680-47990730	HIPEpiC	eye:	n/a
39	chr7:47990680-47990730	T-47D	breast:	n/a
40	chr7:47990680-47990730	HUVEC	blood vessel:	n/a
41	chr7:47990680-47990730	AG10803	skin:	n/a
42	chr7:47990680-47990730	AG04450	lung:	fetal
43	chr7:47990680-47990730	MCF-7	breast:	n/a
44	chr7:47990680-47990730	HepG2	liver:	n/a
45	chr7:47990680-47990730	BJ	skin:	n/a
46	chr7:47990680-47990730	AG09319	gingival:	n/a
47	chr7:47990680-47990730	H1-hESC	embryonic stem cell:	embryo
48	chr7:47990680-47990730	HNPCEpiC	eye:	n/a
49	chr7:47990680-47990730	HL-60	blood:	n/a
50	chr7:47990680-47990730	ovcar-3	ovarian:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:47988986..47991046-chr7:48004400..48006975,2	MCF-7	breast:

No data

Variant related genes	Relation type
PKD1L1	TF binding region
PKD1L1	CpG island

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1056663	0.88[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12702401	0.87[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13309127	0.84[AMR][1000 genomes]
rs1879833	0.89[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.95[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1879834	0.88[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2037483	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2037485	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2242477	0.84[CEU][hapmap];0.85[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs2242478	0.84[CEU][hapmap];0.85[CHB][hapmap];0.87[JPT][hapmap];0.95[YRI][hapmap]
rs2242479	0.85[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.95[YRI][hapmap];0.80[EUR][1000 genomes]
rs2686816	0.89[CHB][hapmap]
rs2686821	0.81[CEU][hapmap]
rs2686823	0.81[CEU][hapmap]
rs2686830	0.88[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2686831	0.88[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2686832	0.88[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2686833	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2686834	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2686835	0.88[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2686836	0.89[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2686838	0.88[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2686839	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2686841	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2708853	0.81[AFR][1000 genomes]
rs2708858	0.89[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs2708859	0.80[EUR][1000 genomes]
rs2708861	0.84[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs2708862	0.88[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2708873	0.82[CEU][hapmap];0.95[CHB][hapmap];0.86[AFR][1000 genomes]
rs2708877	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2708882	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2708894	0.88[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2708895	0.88[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2708896	0.84[CEU][hapmap]
rs2708897	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2708898	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2708902	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2708903	0.88[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2708905	0.84[CEU][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2708911	0.81[CEU][hapmap]
rs2952720	0.81[AMR][1000 genomes]
rs3176478	0.85[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3176564	0.87[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.95[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34016848	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35151200	0.88[AFR][1000 genomes]
rs35536957	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4720624	0.81[CHB][hapmap]
rs885337	0.85[CEU][hapmap]
rs939904	0.81[CEU][hapmap]
rs939905	0.82[CEU][hapmap]
rs953572	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9648569	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026223	chr7:47560728-48243287	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv869585	chr7:47765428-48151324	Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv830991	chr7:47854530-48025996	Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv532120	chr7:47882757-48195869	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv470221	chr7:47917495-48354363	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv464442	chr7:47917495-48354820	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv606893	chr7:47917495-48354820	Flanking Active TSS Strong transcription Genic enhancers Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2708875	UPP1	cis	Muscle Skeletal	GTEx
rs2708875	UPP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:47934000-48001800	Weak transcription	Psoas Muscle	Psoas
2	chr7:47967600-47993400	Weak transcription	Brain Anterior Caudate	brain
3	chr7:47977400-48000600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr7:47978400-47993800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr7:47978400-47994000	Weak transcription	Fetal Thymus	thymus
6	chr7:47978600-47992600	Weak transcription	Primary B cells from cord blood	blood
7	chr7:47980600-47994200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr7:47980800-47993000	Weak transcription	Fetal Stomach	stomach
9	chr7:47981200-47991400	Weak transcription	Colonic Mucosa	Colon
10	chr7:47981200-47995600	Weak transcription	Aorta	Aorta
11	chr7:47981800-47990800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr7:47981800-47991200	Weak transcription	A549	lung
13	chr7:47981800-47991600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr7:47982000-47994000	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr7:47982000-47994000	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr7:47982000-47994200	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr7:47982000-47999400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr7:47982400-47992600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr7:47983600-47993600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr7:47983600-47993800	Weak transcription	Osteobl	bone
21	chr7:47983600-47994400	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr7:47983600-48001000	Weak transcription	NHLF	lung
23	chr7:47983800-47993600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr7:47983800-47993800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr7:47983800-47995800	Weak transcription	NHDF-Ad	bronchial
26	chr7:47984800-47993800	Weak transcription	Esophagus	oesophagus
27	chr7:47984800-47996000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr7:47985000-48001400	Weak transcription	Hela-S3	cervix
29	chr7:47985200-47995000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr7:47985200-47995400	Weak transcription	Fetal Heart	heart
31	chr7:47985400-47993800	Weak transcription	Placenta	Placenta
32	chr7:47985400-47995800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr7:47985600-48000600	Weak transcription	Ovary	ovary
34	chr7:47986200-47991200	Weak transcription	Fetal Kidney	kidney
35	chr7:47986200-47991400	Weak transcription	Pancreas	Pancrea
36	chr7:47986400-47991200	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr7:47986400-47991200	Enhancers	HUVEC	blood vessel
38	chr7:47986400-47993000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr7:47986400-47993400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr7:47986400-47993800	Weak transcription	HMEC	breast
41	chr7:47986400-47994200	Weak transcription	Small Intestine	intestine
42	chr7:47986400-48003800	Weak transcription	Fetal Brain Male	brain
43	chr7:47986600-47993600	Weak transcription	Duodenum Mucosa	Duodenum
44	chr7:47986600-47994000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr7:47986800-48001800	Weak transcription	NHEK	skin
46	chr7:47987200-47993200	Weak transcription	Fetal Intestine Small	intestine
47	chr7:47987200-47993800	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr7:47987200-47994400	Weak transcription	Right Ventricle	heart
49	chr7:47987800-47994000	Weak transcription	Lung	lung
50	chr7:47988200-47993400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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