Variant report

Variant	rs16841874
Chromosome Location	chr3:99720564-99720565
allele	A/C
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:99708217..99709816-chr3:99718365..99721213,2	MCF-7	breast:
2	chr3:99705385..99708827-chr3:99720207..99724283,4	MCF-7	breast:
3	chr3:99720235..99722178-chr3:99725439..99727332,2	MCF-7	breast:
4	chr3:99592235..99595057-chr3:99720333..99721869,2	MCF-7	breast:
5	chr3:99618971..99621795-chr3:99720299..99722726,2	MCF-7	breast:
6	chr3:99720503..99722744-chr3:99759089..99760779,2	MCF-7	breast:
7	chr3:99719980..99722131-chr3:99722963..99725848,2	K562	blood:
8	chr3:99594649..99596564-chr3:99719153..99720665,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000168386	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11711935	0.83[LWK][hapmap];0.90[MKK][hapmap]
rs11719468	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.81[EUR][1000 genomes]
rs12488245	0.81[CEU][hapmap]
rs13059754	0.84[CEU][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.81[MKK][hapmap]
rs1384062	0.84[CEU][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap]
rs1387647	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap]
rs1718235	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2316263	0.80[CEU][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap]
rs35422475	0.85[ASN][1000 genomes]
rs4577503	0.84[CEU][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.83[MKK][hapmap]
rs4928150	0.84[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap]
rs4928151	0.84[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs4928153	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap]
rs4928230	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs4928235	0.85[ASN][1000 genomes]
rs4928237	0.84[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs58704213	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6440967	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs6788750	0.88[LWK][hapmap];0.94[MKK][hapmap]
rs6802817	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs6806323	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs6808765	0.81[ASN][1000 genomes]
rs7619512	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7649349	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs7650727	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs766778	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs793439	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs793443	0.84[CEU][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap]
rs793446	0.84[CEU][hapmap];0.94[JPT][hapmap]
rs793450	0.90[LWK][hapmap];0.89[MKK][hapmap];0.85[YRI][hapmap]
rs793464	0.84[CEU][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.83[MKK][hapmap]
rs793469	0.90[LWK][hapmap];0.92[MKK][hapmap];0.85[YRI][hapmap]
rs793475	0.84[CEU][hapmap];0.93[JPT][hapmap]
rs793502	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs796976	0.84[CEU][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap]
rs813218	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs902159	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs923472	0.84[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs9847283	0.80[CEU][hapmap]

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	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv932634	chr3:99660690-99888854	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010579	chr3:99660754-99901817	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1008483	chr3:99660754-99903769	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1010897	chr3:99660754-99904783	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1001529	chr3:99661758-99892654	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
9	nsv536665	chr3:99661758-99892654	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
10	nsv999332	chr3:99690207-99774720	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16841874	OR5H6	cis	cerebellum	SCAN
rs16841874	SENP7	cis	parietal	SCAN
rs16841874	C3orf26	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99708400-99724600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:99713600-99787800	Weak transcription	Primary T cells from cord blood	blood
3	chr3:99714000-99720600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:99714600-99724400	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr3:99714800-99720800	Weak transcription	Fetal Intestine Small	intestine
6	chr3:99714800-99724600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:99715800-99724200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr3:99716400-99758800	Weak transcription	Primary B cells from cord blood	blood
9	chr3:99716800-99721400	Weak transcription	HUVEC	blood vessel
10	chr3:99717000-99720800	Weak transcription	NH-A	brain
11	chr3:99718200-99720600	Weak transcription	Psoas Muscle	Psoas
12	chr3:99718200-99723000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:99718600-99721200	Weak transcription	NHDF-Ad	bronchial
14	chr3:99718800-99720600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr3:99718800-99721400	Weak transcription	Osteobl	bone
16	chr3:99719000-99721200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:99719000-99721400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:99719200-99723200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:99719400-99721200	Weak transcription	HepG2	liver
20	chr3:99719400-99721800	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr3:99719800-99721000	Enhancers	Placenta Amnion	Placenta Amnion
22	chr3:99719800-99723000	Enhancers	HMEC	breast
23	chr3:99720200-99720600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr3:99720200-99720800	Enhancers	Fetal Kidney	kidney
25	chr3:99720200-99721800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:99720200-99721800	Flanking Active TSS	NHEK	skin
27	chr3:99720200-99727600	Enhancers	Stomach Mucosa	stomach
28	chr3:99720400-99720600	Enhancers	Colon Smooth Muscle	Colon
29	chr3:99720400-99720800	Enhancers	Rectal Mucosa Donor 29	rectum
30	chr3:99720400-99720800	Strong transcription	Skeletal Muscle Female	skeletal muscle
31	chr3:99720400-99721000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr3:99720400-99722600	Enhancers	Duodenum Mucosa	Duodenum
33	chr3:99720400-99723000	Enhancers	Hela-S3	cervix

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