Variant report

Variant	rs3176581
Chromosome Location	chr7:48008738-48008739
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:47892179..47892957-chr7:48008189..48008911,2	K562	blood:
2	chr7:47305137..47306030-chr7:48008488..48008989,2	K562	blood:
3	chr7:48008107..48009106-chr7:48149515..48150029,2	MCF-7	breast:
4	chr7:47884198..47887290-chr7:48007408..48010423,4	MCF-7	breast:
5	chr7:47984519..47985336-chr7:48008536..48009073,2	MCF-7	breast:
6	chr7:47984273..47985665-chr7:48007663..48009312,11	MCF-7	breast:
7	chr7:48007920..48009959-chr7:48011968..48013764,2	MCF-7	breast:
8	chr7:48008512..48011400-chr7:48014003..48016517,2	MCF-7	breast:
9	chr7:47984581..47985500-chr7:48008161..48008952,2	K562	blood:
10	chr7:48008475..48011442-chr7:48016740..48019056,3	MCF-7	breast:
11	chr7:48005343..48009057-chr7:48009774..48012451,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000136273	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10261436	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10499669	0.91[ASW][hapmap];0.90[CEU][hapmap];0.88[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];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12667562	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12669119	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17131948	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2307252	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2348665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2686782	0.86[YRI][hapmap]
rs2686792	0.81[YRI][hapmap]
rs3176491	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3176568	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3176595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36213466	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4720625	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56075223	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59023024	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59920101	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62447088	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62447089	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62447093	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73695940	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs885338	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]

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
rs3176581	PKD1L1	cis	cerebellum	SCAN
rs3176581	PKD1L1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:47999400-48008800	Strong transcription	H1 Cell Line	embryonic stem cell
2	chr7:47999600-48017600	Strong transcription	Primary T cells from cord blood	blood
3	chr7:47999600-48018000	Strong transcription	Fetal Thymus	thymus
4	chr7:48000200-48008800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr7:48000200-48008800	Strong transcription	HSMM	muscle
6	chr7:48000200-48009400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr7:48000200-48009400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr7:48000200-48016600	Strong transcription	Liver	Liver
9	chr7:48000200-48017800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr7:48000400-48008800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr7:48000400-48008800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr7:48000400-48009000	Strong transcription	Primary B cells from peripheral blood	blood
13	chr7:48000400-48009000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr7:48000400-48009000	Strong transcription	Fetal Intestine Large	intestine
15	chr7:48000400-48009400	Strong transcription	Osteobl	bone
16	chr7:48000400-48009600	Strong transcription	A549	lung
17	chr7:48000400-48010000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr7:48000400-48011200	Strong transcription	Colon Smooth Muscle	Colon
19	chr7:48000400-48016800	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr7:48000400-48017600	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr7:48000400-48017600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr7:48000400-48017600	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr7:48000400-48017800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr7:48000400-48017800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr7:48000600-48008800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr7:48000600-48009200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr7:48000600-48009200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr7:48000600-48009200	Strong transcription	Muscle Satellite Cultured Cells	--
29	chr7:48000600-48009400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr7:48000600-48009400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr7:48000600-48009400	Strong transcription	Thymus	Thymus
32	chr7:48000600-48009600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr7:48000600-48009600	Strong transcription	Fetal Muscle Trunk	muscle
34	chr7:48000600-48010000	Strong transcription	NHDF-Ad	bronchial
35	chr7:48000600-48010200	Strong transcription	Fetal Muscle Leg	muscle
36	chr7:48000600-48011200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
37	chr7:48000600-48011400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr7:48000600-48015800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr7:48000600-48017600	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr7:48001000-48009400	Strong transcription	NHLF	lung
41	chr7:48001000-48009800	Strong transcription	Fetal Intestine Small	intestine
42	chr7:48001200-48009400	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr7:48001400-48009000	Strong transcription	Hela-S3	cervix
44	chr7:48001600-48017600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr7:48001800-48009200	Strong transcription	NHEK	skin
46	chr7:48002000-48009400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr7:48002000-48018200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr7:48002200-48009000	Strong transcription	HMEC	breast
49	chr7:48003600-48008800	Strong transcription	Rectal Smooth Muscle	rectum
50	chr7:48004000-48008800	Strong transcription	K562	blood

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