Variant report

Variant	rs12453935
Chromosome Location	chr17:59897455-59897456
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:58677576..58679804-chr17:59895961..59897997,2	MCF-7	breast:
2	chr17:59488207..59489907-chr17:59897197..59900125,2	MCF-7	breast:
3	chr1:107598419..107600523-chr17:59895411..59897981,2	MCF-7	breast:
4	chr17:59897032..59900869-chr17:59902920..59905973,5	MCF-7	breast:
5	chr17:59895734..59897496-chr17:59940156..59941958,2	K562	blood:
6	chr17:59895324..59898456-chr17:59898526..59902353,6	MCF-7	breast:
7	chr17:59890246..59897512-chr17:59906301..59911865,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198890	Chromatin interaction
ENSG00000136492	Chromatin interaction
ENSG00000187013	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000170836	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1015771	0.92[CHB][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap]
rs10438771	0.84[MEX][hapmap]
rs10468558	0.84[MEX][hapmap]
rs10515211	1.00[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10515212	0.87[CEU][hapmap]
rs11079445	0.84[MEX][hapmap]
rs11650471	0.84[MEX][hapmap]
rs11652477	0.87[CEU][hapmap]
rs11653175	0.82[AMR][1000 genomes]
rs11658539	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11871753	0.92[CHB][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap]
rs12452396	0.93[CEU][hapmap]
rs12453801	0.84[MEX][hapmap]
rs12453966	0.84[MEX][hapmap]
rs12603617	0.84[MEX][hapmap]
rs12948762	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12949659	1.00[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1468577	1.00[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs17542001	0.87[CEU][hapmap]
rs17614124	0.87[CEU][hapmap]
rs1978244	1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1990337	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1990338	1.00[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2066962	0.87[CEU][hapmap]
rs2191249	0.86[CHB][hapmap];0.87[GIH][hapmap];0.92[MEX][hapmap]
rs2278813	0.87[CEU][hapmap]
rs2378905	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2378906	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2890021	0.86[CHB][hapmap]
rs4968582	0.83[MEX][hapmap]
rs62068837	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6504066	0.80[MEX][hapmap]
rs6504068	0.85[CHB][hapmap]
rs6504070	0.82[ASN][1000 genomes]
rs6504071	1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes]
rs6504072	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs717961	0.80[MEX][hapmap]
rs7207074	0.80[MEX][hapmap]
rs7207881	0.92[CHB][hapmap];0.94[JPT][hapmap]
rs7208704	0.93[JPT][hapmap]
rs7212172	1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.83[ASN][1000 genomes]
rs7213329	1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.83[ASN][1000 genomes]
rs7213587	0.80[MEX][hapmap]
rs7214884	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7215784	1.00[CHB][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7216011	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7216756	1.00[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7216824	0.83[ASN][1000 genomes]
rs7217206	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7220688	0.80[MEX][hapmap]
rs7220719	0.80[MEX][hapmap]
rs7222799	1.00[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7223607	0.87[CEU][hapmap]
rs8075370	0.80[MEX][hapmap]
rs8075585	0.87[CEU][hapmap]
rs8076727	0.87[CEU][hapmap]
rs8076746	0.93[CEU][hapmap]
rs8077088	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs8078977	1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs9303449	0.84[MEX][hapmap]
rs9895987	1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9897121	1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9897928	0.92[CHB][hapmap];0.94[JPT][hapmap]
rs9900559	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9902995	0.86[CHB][hapmap];0.87[GIH][hapmap];0.92[MEX][hapmap]
rs9904292	1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9906313	0.92[CHB][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap]
rs9907299	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs991378	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3378293	chr17:59744117-60124899	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv908673	chr17:59767501-59926645	Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	94 gene(s)	inside rSNPs	diseases
3	nsv908674	chr17:59800827-59899790	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
4	nsv575841	chr17:59812748-59914681	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
5	nsv575842	chr17:59812748-59927307	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	70 gene(s)	inside rSNPs	diseases
6	nsv908675	chr17:59835864-59937286	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
7	esv1794309	chr17:59861640-59907952	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region Chromatin interactive region	32 gene(s)	inside rSNPs	diseases
8	esv1827960	chr17:59869069-59897455	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region	27 gene(s)	inside rSNPs	diseases
9	nsv575843	chr17:59869081-59935723	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
10	nsv916786	chr17:59890834-60103687	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Lung function (forced expiratory flow between 25% and 75% of forced vital capacity)	24023788	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12453935	BRIP1	cis	parietal	SCAN
rs12453935	PTRH2	cis	cerebellum	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59825800-59898400	Weak transcription	Thymus	Thymus
2	chr17:59848800-59911200	Weak transcription	HUVEC	blood vessel
3	chr17:59851200-59902600	Weak transcription	Fetal Stomach	stomach
4	chr17:59852600-59898000	Weak transcription	Fetal Intestine Small	intestine
5	chr17:59863600-59925000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr17:59869200-59898200	Weak transcription	Fetal Muscle Leg	muscle
7	chr17:59870400-59933400	Weak transcription	Fetal Intestine Large	intestine
8	chr17:59873200-59905000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr17:59874400-59910600	Weak transcription	Hela-S3	cervix
10	chr17:59879400-59898000	Weak transcription	Fetal Thymus	thymus
11	chr17:59881000-59898400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr17:59883600-59898400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr17:59883800-59898400	Weak transcription	A549	lung
14	chr17:59884200-59933200	Weak transcription	K562	blood
15	chr17:59884400-59898000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr17:59887400-59901600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr17:59887600-59898200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr17:59887600-59898400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr17:59887600-59899800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr17:59887600-59905200	Weak transcription	Fetal Lung	lung
21	chr17:59887800-59898000	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr17:59887800-59911000	Weak transcription	NH-A	brain
23	chr17:59888000-59898400	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr17:59888000-59898400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr17:59888000-59910400	Weak transcription	NHEK	skin
26	chr17:59888000-59911000	Weak transcription	NHLF	lung
27	chr17:59888000-59911400	Weak transcription	HSMM	muscle
28	chr17:59889000-59898400	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr17:59889200-59898000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr17:59889200-59898000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr17:59889400-59898400	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr17:59889600-59898600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr17:59890600-59897600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr17:59891000-59897800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr17:59891000-59905200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr17:59891000-59911000	Weak transcription	NHDF-Ad	bronchial
37	chr17:59894000-59897800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr17:59894000-59898000	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr17:59894000-59905200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr17:59894000-59905400	Weak transcription	HepG2	liver
41	chr17:59894000-59910600	Weak transcription	HMEC	breast
42	chr17:59894000-59922400	Weak transcription	Osteobl	bone
43	chr17:59894200-59899000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr17:59894400-59897600	Weak transcription	GM12878-XiMat	blood
45	chr17:59894400-59897800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr17:59894400-59897800	Weak transcription	Primary hematopoietic stem cells	blood
47	chr17:59894600-59897800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr17:59894600-59898200	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr17:59894800-59897600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr17:59894800-59897600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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