Variant report

Variant	rs3098177
Chromosome Location	chr15:50783777-50783778
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFYA	chr15:50783712-50783902	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:50645564..50647372-chr15:50783247..50786142,2	MCF-7	breast:
2	chr15:50647443..50649396-chr15:50783549..50786868,3	MCF-7	breast:
3	chr15:50646598..50648550-chr15:50782199..50785189,3	K562	blood:
4	chr15:50781518..50783831-chr15:50786910..50789444,2	MCF-7	breast:

Variant related genes	Relation type
USP8	TF binding region
ENSG00000244879	Chromatin interaction
ENSG00000104064	Chromatin interaction
ENSG00000259618	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11070776	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11070784	0.80[CHD][hapmap]
rs12593481	0.82[ASN][1000 genomes]
rs2289108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28582911	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3098167	0.87[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs3098168	0.85[CEU][hapmap];0.82[YRI][hapmap]
rs3098169	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3098171	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3098174	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3098179	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3098180	0.83[CHB][hapmap]
rs3098183	0.91[CHB][hapmap]
rs3098190	0.86[CHB][hapmap]
rs3098194	0.86[CHB][hapmap]
rs3098198	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs3098205	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs3109887	0.86[CHB][hapmap]
rs3131559	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3131560	1.00[ASW][hapmap];0.80[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.94[MKK][hapmap];0.87[TSI][hapmap];0.82[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3131562	0.88[ASW][hapmap];0.92[CEU][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3131565	0.83[CHB][hapmap]
rs3131566	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3131567	0.84[CEU][hapmap]
rs3131568	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3131574	0.90[ASN][1000 genomes]
rs3131609	0.91[CHB][hapmap]
rs3131613	0.83[CHB][hapmap]
rs4318151	0.96[CEU][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs512708	0.80[CHB][hapmap]
rs56398519	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs679774	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs7170543	0.86[CHB][hapmap]
rs7174015	0.87[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8026653	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045456	chr15:50592472-51019873	Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
2	nsv948579	chr15:50645530-51045564	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
3	nsv524613	chr15:50656449-50868779	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv904210	chr15:50702058-50786024	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv1040717	chr15:50715572-50846521	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv1053966	chr15:50715572-51133186	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
7	nsv542383	chr15:50715572-51133186	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
8	nsv1043805	chr15:50715572-51208891	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
9	nsv542384	chr15:50715572-51208891	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
10	nsv1049576	chr15:50744781-50843495	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	nsv1047443	chr15:50744781-51647023	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
12	nsv1051990	chr15:50745814-51133186	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
13	nsv1054970	chr15:50761410-51036625	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
14	nsv457134	chr15:50770868-51184583	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
15	nsv471242	chr15:50770868-51184583	Genic enhancers ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
16	nsv569396	chr15:50770868-51184583	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
17	nsv457135	chr15:50770868-51189707	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
18	nsv569397	chr15:50770868-51189707	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
19	nsv1048621	chr15:50775451-51115535	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
20	nsv1047039	chr15:50782070-51187804	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
21	nsv542385	chr15:50782070-51187804	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50733400-50785200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:50734000-50785600	Weak transcription	Fetal Brain Male	brain
3	chr15:50738200-50796800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr15:50741800-50797000	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr15:50744000-50789000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr15:50746200-50794400	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr15:50748400-50785200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:50750000-50794400	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr15:50751000-50792400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr15:50751000-50796600	Strong transcription	Fetal Thymus	thymus
11	chr15:50754400-50797000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr15:50756000-50785200	Weak transcription	Small Intestine	intestine
13	chr15:50756600-50785000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr15:50756600-50795800	Strong transcription	Adipose Nuclei	Adipose
15	chr15:50757000-50796600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr15:50757000-50796800	Strong transcription	Liver	Liver
17	chr15:50761800-50794000	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr15:50762400-50794000	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr15:50763000-50795800	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr15:50763600-50796200	Strong transcription	Primary T cells from cord blood	blood
21	chr15:50764800-50785200	Weak transcription	Esophagus	oesophagus
22	chr15:50764800-50787000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr15:50767200-50784600	Weak transcription	Spleen	Spleen
24	chr15:50767400-50785200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr15:50768000-50796800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr15:50768200-50794000	Strong transcription	Skeletal Muscle Female	skeletal muscle
27	chr15:50768400-50797000	Strong transcription	Duodenum Mucosa	Duodenum
28	chr15:50768400-50797000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr15:50768800-50796000	Strong transcription	Hela-S3	cervix
30	chr15:50770200-50794000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr15:50771200-50796000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr15:50772400-50796000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr15:50772600-50784600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr15:50772800-50796000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr15:50773400-50785200	Weak transcription	Aorta	Aorta
36	chr15:50774200-50797600	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr15:50774400-50785200	Weak transcription	Brain Angular Gyrus	brain
38	chr15:50775400-50783800	Weak transcription	Psoas Muscle	Psoas
39	chr15:50775600-50795400	Weak transcription	Stomach Mucosa	stomach
40	chr15:50776000-50796000	Strong transcription	Fetal Intestine Large	intestine
41	chr15:50776400-50789400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr15:50776400-50792400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr15:50776400-50796000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr15:50777000-50796000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr15:50777200-50791600	Strong transcription	Fetal Muscle Leg	muscle
46	chr15:50777400-50796000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr15:50777800-50789200	Strong transcription	Fetal Stomach	stomach
48	chr15:50777800-50789600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr15:50778200-50784600	Weak transcription	Brain Germinal Matrix	brain
50	chr15:50778200-50786600	Strong transcription	Sigmoid Colon	Sigmoid Colon

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