Variant report

Variant	rs1005655
Chromosome Location	chr17:45919465-45919466
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:61)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr17:45919380-45919530	GM12872	blood:	n/a	n/a
2	HCFC1	chr17:45917644-45919543	Hela-S3	cervix:	n/a	n/a
3	EBF1	chr17:45919449-45919550	GM12878	blood:	n/a	n/a
4	IRF1	chr17:45919373-45919556	K562	blood:	n/a	n/a
5	CTCF	chr17:45917798-45919836	SK-N-SH	brain:	n/a	chr17:45918728-45918738 chr17:45918726-45918735 chr17:45918726-45918739
6	STAT3	chr17:45919430-45919556	GM12878	blood:	n/a	n/a
7	SMC3	chr17:45917380-45919880	SK-N-SH	brain:	n/a	chr17:45918729-45918739
8	CTCF	chr17:45919320-45919470	HRPEpiC	eye:	n/a	n/a
9	RUNX3	chr17:45919256-45919729	GM12878	blood:	n/a	n/a
10	CTCF	chr17:45917785-45920041	A549	lung:	n/a	chr17:45918728-45918738 chr17:45918726-45918735 chr17:45918726-45918739

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr17:45919419-45919469	AG04450	lung:	fetal
2	chr17:45919419-45919469	AG09319	gingival:	n/a
3	chr17:45919419-45919469	HIPEpiC	eye:	n/a
4	chr17:45919419-45919469	ProgFib	skin:	n/a
5	chr17:45919419-45919469	T-47D	breast:	n/a
6	chr17:45919419-45919469	HCT-116	colon:	n/a
7	chr17:45919419-45919469	HAEpiC	amniotic membrane:	n/a
8	chr17:45919419-45919469	Jurkat	blood:	n/a
9	chr17:45919419-45919469	HPAEpiC	pulmonary alveolar:	n/a
10	chr17:45919419-45919469	Hela-S3	cervix:	n/a
11	chr17:45919419-45919469	NT2-D1	testis:	n/a
12	chr17:45919419-45919469	CMK	blood:	n/a
13	chr17:45919419-45919469	SK-N-SH_RA	brain:	n/a
14	chr17:45919419-45919469	NB4	blood:	n/a
15	chr17:45919419-45919469	HL-60	blood:	n/a
16	chr17:45919419-45919469	BE2_C	brain:	n/a
17	chr17:45919419-45919469	HCPEpiC	choroid plexus:	n/a
18	chr17:45919419-45919469	NHBE	bronchial:	n/a
19	chr17:45919419-45919469	ovcar-3	ovarian:	n/a
20	chr17:45919419-45919469	BJ	skin:	n/a
21	chr17:45919419-45919469	U87	brain:	n/a
22	chr17:45919419-45919469	SAEC	small airway:	n/a
23	chr17:45919419-45919469	LNCaP	prostate:	n/a
24	chr17:45919419-45919469	HMEC	breast:	n/a
25	chr17:45919419-45919469	HCF	heart:	n/a
26	chr17:45919419-45919469	AG09309	skin:	n/a
27	chr17:45919419-45919469	IMR90	lung:	fetal
28	chr17:45919419-45919469	RPTEC	kidney:	n/a
29	chr17:45919419-45919469	AoSMC	blood vessel:	n/a
30	chr17:45919419-45919469	ECC-1	luminal epithelium:	n/a
31	chr17:45919419-45919469	AG04449	skin:	fetal
32	chr17:45919419-45919469	GM12892	blood:	n/a
33	chr17:45919419-45919469	PrEC	prostate:	n/a
34	chr17:45919419-45919469	HUVEC	blood vessel:	n/a
35	chr17:45919419-45919469	NHDF-neo	bronchial:	n/a
36	chr17:45919419-45919469	AG10803	skin:	n/a
37	chr17:45919419-45919469	H1-hESC	embryonic stem cell:	embryo
38	chr17:45919419-45919469	HCM	heart:	n/a
39	chr17:45919419-45919469	PFSK-1	brain:	n/a
40	chr17:45919419-45919469	HRCEpiC	kidney:	n/a
41	chr17:45919419-45919469	HRE	kidney:	n/a
42	chr17:45919419-45919469	PANC-1	pancreas:	n/a
43	chr17:45919419-45919469	A549	lung:	n/a
44	chr17:45919419-45919469	SKMC	muscle:	n/a
45	chr17:45919419-45919469	SK-N-MC	brain:	n/a
46	chr17:45919419-45919469	NH-A	brain:	n/a
47	chr17:45919419-45919469	Caco-2	colon:	n/a
48	chr17:45919419-45919469	GM12878	blood:	n/a
49	chr17:45919419-45919469	MCF-7	breast:	n/a
50	chr17:45919419-45919469	HRPEpiC	eye:	n/a

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:45917528..45920214-chr17:46032690..46035678,3	MCF-7	breast:
2	chr17:45918850..45921918-chr17:45964837..45968341,4	K562	blood:
3	chr17:45918236..45922252-chr17:45971224..45975227,6	K562	blood:
4	chr17:45916146..45920179-chr17:45971137..45974158,6	K562	blood:
5	chr17:45918878..45920635-chr17:45927299..45929830,2	MCF-7	breast:
6	chr17:45918706..45921396-chr17:45943154..45946269,3	K562	blood:
7	chr17:45915230..45925590-chr17:45966201..45976437,35	MCF-7	breast:
8	chr17:45906340..45909429-chr17:45918735..45922764,3	K562	blood:
9	chr17:45914114..45922201-chr17:45959661..45964608,11	MCF-7	breast:
10	chr17:45917897..45920844-chr17:46033567..46035986,3	MCF-7	breast:
11	chr17:45913484..45922782-chr17:45969196..45975741,24	MCF-7	breast:
12	chr17:45917724..45920476-chr17:46044625..46046608,2	MCF-7	breast:

No data

Variant related genes	Relation type
SCRN2	TF binding region
SCRN2	CpG island
ENSG00000167182	Chromatin interaction
ENSG00000266821	Chromatin interaction
ENSG00000141294	Chromatin interaction
ENSG00000108465	Chromatin interaction
ENSG00000159111	Chromatin interaction
ENSG00000167183	Chromatin interaction
ENSG00000264920	Chromatin interaction
ENSG00000189120	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs11079795	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11079796	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];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11650289	0.95[CHB][hapmap];0.91[JPT][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11650536	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];1.00[TSI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11652439	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11869958	0.95[CHB][hapmap]
rs11870002	0.95[CHB][hapmap]
rs16948401	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16948590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16948722	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]
rs1985407	0.89[CHB][hapmap]
rs2001380	0.82[EUR][1000 genomes]
rs2001381	0.81[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs2074188	0.95[CHB][hapmap]
rs2074189	0.95[CHB][hapmap]
rs3809869	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4794203	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs701984	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];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72833426	0.87[ASN][1000 genomes]
rs8075360	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs878171	0.86[CHB][hapmap]
rs9674817	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv908573	chr17:45858487-45956073	Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv908574	chr17:45876022-45930584	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv517880	chr17:45887951-45933341	Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv518892	chr17:45887951-46029432	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1005655	SNX11	cis	parietal	SCAN
rs1005655	OSBPL7	cis	Thyroid	GTEx
rs1005655	CALCOCO2	cis	parietal	SCAN
rs1005655	SCRN2	cis	Whole Blood	GTEx
rs1005655	RPL27	cis	cerebellum	SCAN
rs1005655	VAT1	cis	cerebellum	SCAN
rs1005655	SCRN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45918600-45922600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr17:45918800-45919600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr17:45918800-45919600	Enhancers	Primary B cells from peripheral blood	blood
4	chr17:45918800-45919600	Flanking Active TSS	Liver	Liver
5	chr17:45918800-45919800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
6	chr17:45918800-45919800	Flanking Active TSS	Duodenum Mucosa	Duodenum
7	chr17:45918800-45919800	Enhancers	Placenta	Placenta
8	chr17:45918800-45919800	Enhancers	Fetal Thymus	thymus
9	chr17:45918800-45919800	Enhancers	HMEC	breast
10	chr17:45918800-45920600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr17:45918800-45921000	Enhancers	Rectal Mucosa Donor 29	rectum
12	chr17:45918800-45921200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr17:45918800-45921200	Enhancers	Colonic Mucosa	Colon
14	chr17:45918800-45921200	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr17:45918800-45922400	Enhancers	Fetal Intestine Large	intestine
16	chr17:45918800-45924600	Weak transcription	Spleen	Spleen
17	chr17:45919000-45919600	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr17:45919000-45919600	Weak transcription	Gastric	stomach
19	chr17:45919000-45919600	Enhancers	NHEK	skin
20	chr17:45919000-45919800	Enhancers	Primary T cells from cord blood	blood
21	chr17:45919000-45919800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr17:45919000-45919800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr17:45919000-45919800	Enhancers	Fetal Kidney	kidney
24	chr17:45919000-45919800	Enhancers	Fetal Lung	lung
25	chr17:45919000-45919800	Enhancers	K562	blood
26	chr17:45919000-45920000	Enhancers	Brain Anterior Caudate	brain
27	chr17:45919000-45920200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr17:45919000-45920200	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr17:45919000-45920200	Enhancers	Primary T cells fromperipheralblood	blood
30	chr17:45919000-45920200	Weak transcription	NHDF-Ad	bronchial
31	chr17:45919000-45920400	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr17:45919000-45920400	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr17:45919000-45920400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr17:45919000-45920400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr17:45919000-45920400	Weak transcription	Brain Angular Gyrus	brain
36	chr17:45919000-45920600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr17:45919000-45920600	Weak transcription	Osteobl	bone
38	chr17:45919000-45920800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr17:45919000-45920800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr17:45919000-45920800	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr17:45919000-45920800	Enhancers	Fetal Stomach	stomach
42	chr17:45919000-45921000	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr17:45919000-45921000	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr17:45919000-45921000	Enhancers	A549	lung
45	chr17:45919000-45921200	Flanking Active TSS	HepG2	liver
46	chr17:45919000-45921600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr17:45919000-45921800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr17:45919000-45921800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr17:45919000-45922000	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr17:45919000-45922200	Enhancers	Fetal Intestine Small	intestine

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