Variant report

Variant	rs17816519
Chromosome Location	chr15:33205006-33205007
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:33203701..33205590-chr15:33205602..33207495,2	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10152541	1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1020558	0.98[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10519764	0.84[ASW][hapmap];0.87[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.81[TSI][hapmap];0.84[YRI][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10519765	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11629687	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11629899	0.91[CEU][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11631608	0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11632728	0.85[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11633554	0.90[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11635920	0.82[CEU][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11635965	0.92[ASW][hapmap];0.82[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.84[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11637250	0.84[YRI][hapmap]
rs11637646	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12899881	0.82[CEU][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12904054	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12905485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12909023	0.95[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs12913108	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13379651	0.90[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];0.98[ASN][1000 genomes]
rs1376791	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.84[YRI][hapmap];0.98[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16961209	0.86[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs17228908	0.86[MEX][hapmap]
rs17228929	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[MEX][hapmap];0.98[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17228971	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17816555	1.00[ASW][hapmap];0.86[CEU][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];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1993132	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1993133	0.92[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2339163	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs347921	0.82[CHB][hapmap];0.95[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs35639096	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35937803	0.88[ASN][1000 genomes]
rs36100673	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3812926	0.92[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.84[TSI][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62003760	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7178559	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72719313	0.88[ASN][1000 genomes]
rs9806422	0.87[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9806436	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422296	chr15:32798938-33221215	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv456785	chr15:32926076-33352989	Genic enhancers Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv568913	chr15:32926076-33352989	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv832962	chr15:33111517-33239736	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv903978	chr15:33144202-33308641	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv903979	chr15:33144202-33550256	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv1041609	chr15:33148035-33355999	Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv542339	chr15:33148035-33355999	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv903980	chr15:33149087-33264201	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv1052966	chr15:33149753-33541951	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
11	nsv542340	chr15:33149753-33541951	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
12	nsv568917	chr15:33167171-33304172	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17816519	CLLU1OS	trans	parietal	SCAN
rs17816519	FAN1	cis	parietal	SCAN
rs17816519	ARHGAP11B	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:33154400-33216800	Weak transcription	Fetal Thymus	thymus
2	chr15:33155000-33208200	Weak transcription	Fetal Kidney	kidney
3	chr15:33166200-33211800	Weak transcription	HSMMtube	muscle
4	chr15:33191000-33210800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:33191800-33214600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr15:33192400-33210600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr15:33192600-33210800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr15:33195000-33215000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr15:33197600-33219000	Weak transcription	Placenta	Placenta
10	chr15:33197800-33217400	Weak transcription	Lung	lung
11	chr15:33198200-33207200	Weak transcription	Thymus	Thymus
12	chr15:33199200-33212800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr15:33200200-33205600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr15:33200200-33205600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr15:33200600-33208600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr15:33200600-33210800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr15:33200800-33214200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr15:33201200-33207800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr15:33201400-33210400	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr15:33202000-33205800	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr15:33202200-33205800	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr15:33202400-33210000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr15:33202600-33205600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr15:33202600-33210400	Weak transcription	Osteobl	bone
25	chr15:33202600-33211800	Weak transcription	NH-A	brain
26	chr15:33202600-33212000	Weak transcription	HSMM	muscle
27	chr15:33202600-33224600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr15:33202800-33210400	Weak transcription	NHLF	lung
29	chr15:33202800-33215000	Weak transcription	Pancreas	Pancrea
30	chr15:33203200-33210800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr15:33204600-33205200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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