Variant report

Variant	rs3815563
Chromosome Location	chr9:96213146-96213147
allele	A/T
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	TBP	chr9:96213111-96213386	GM12878	blood:	n/a	n/a
2	POLR2A	chr9:96213133-96214099	HepG2	liver:	n/a	n/a
3	HEY1	chr9:96213070-96213289	K562	blood:	n/a	n/a
4	MAX	chr9:96212517-96216356	A549	lung:	n/a	chr9:96212814-96212824
5	POLR2A	chr9:96213098-96215015	HL-60	blood:	n/a	n/a
6	MAZ	chr9:96213076-96214040	GM12878	blood:	n/a	n/a
7	POLR2A	chr9:96213063-96216221	Raji	blood:	n/a	n/a
8	STAT5A	chr9:96213059-96213616	GM12878	blood:	n/a	n/a
9	YY1	chr9:96213119-96215238	SK-N-SH	brain:	n/a	chr9:96214044-96214055 chr9:96214043-96214057 chr9:96215157-96215171 chr9:96214044-96214058 chr9:96213851-96213860 chr9:96214046-96214055 chr9:96213846-96213860
10	MAX	chr9:96212571-96213799	MCF-7	breast:	n/a	chr9:96212814-96212824
11	TBP	chr9:96212733-96216257	K562	blood:	n/a	n/a
12	MAX	chr9:96212572-96214916	HepG2	liver:	n/a	chr9:96212814-96212824
13	POLR2A	chr9:96213046-96214809	K562	blood:	n/a	n/a
14	CTCF	chr9:96213070-96213239	K562	blood:	n/a	chr9:96213092-96213113
15	YY1	chr9:96213022-96215047	GM12878	blood:	n/a	chr9:96214044-96214055 chr9:96214043-96214057 chr9:96214044-96214058 chr9:96213851-96213860 chr9:96214046-96214055 chr9:96213846-96213860
16	CREB1	chr9:96212996-96214137	HepG2	liver:	n/a	n/a
17	POLR2A	chr9:96212631-96214052	GM12891	blood:	n/a	n/a
18	EP300	chr9:96213083-96213312	K562	blood:	n/a	n/a
19	MAX	chr9:96212679-96213392	H1-hESC	embryonic stem cell:	n/a	chr9:96212814-96212824
20	POLR2A	chr9:96212642-96214948	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr9:96213087-96214122	GM12878	blood:	n/a	n/a
22	POLR2A	chr9:96213094-96214794	GM19099	blood:	n/a	n/a
23	WRNIP1	chr9:96212726-96213401	GM12878	blood:	n/a	n/a
24	POLR2A	chr9:96213045-96214952	GM12878	blood:	n/a	n/a
25	MAX	chr9:96213006-96214125	SK-N-SH	brain:	n/a	n/a
26	POLR2A	chr9:96213053-96214931	ECC-1	luminal epithelium:	n/a	n/a
27	POLR2A	chr9:96213097-96214931	MCF-7	breast:	n/a	n/a
28	HEY1	chr9:96213049-96214091	K562	blood:	n/a	n/a
29	RCOR1	chr9:96213093-96213432	GM12878	blood:	n/a	n/a
30	POLR2A	chr9:96213068-96213929	GM12878	blood:	n/a	n/a
31	POLR2A	chr9:96213002-96213402	GM12891	blood:	n/a	n/a
32	TAF1	chr9:96213067-96214088	K562	blood:	n/a	n/a
33	TBP	chr9:96213114-96214011	HepG2	liver:	n/a	n/a
34	YY1	chr9:96213050-96213865	H1-hESC	embryonic stem cell:	n/a	chr9:96213851-96213860 chr9:96213846-96213860
35	MAX	chr9:96212972-96214925	ECC-1	luminal epithelium:	n/a	n/a
36	POLR2A	chr9:96213084-96213300	H1-hESC	embryonic stem cell:	n/a	n/a
37	MYC	chr9:96212612-96216137	K562	blood:	n/a	chr9:96212814-96212824
38	RUNX3	chr9:96213038-96213743	GM12878	blood:	n/a	n/a
39	MAX	chr9:96213144-96213449	HepG2	liver:	n/a	n/a
40	POLR2A	chr9:96212686-96215378	NB4	blood:	n/a	n/a
41	MAX	chr9:96212979-96215010	MCF-7	breast:	n/a	n/a
42	MYC	chr9:96213117-96213347	K562	blood:	n/a	n/a
43	MYC	chr9:96212580-96214647	K562	blood:	n/a	chr9:96212814-96212824
44	POLR2A	chr9:96213017-96213932	GM12891	blood:	n/a	n/a
45	POLR2A	chr9:96213094-96216264	GM18951	blood:	n/a	n/a
46	MAZ	chr9:96213082-96214087	Hela-S3	cervix:	n/a	n/a
47	CHD1	chr9:96212576-96214104	IMR90	lung:	n/a	chr9:96213161-96213168
48	POLR2A	chr9:96212746-96214524	IMR90	lung:	n/a	n/a
49	MYC	chr9:96212594-96214613	MCF10A-Er-Src	breast:	n/a	chr9:96212814-96212824
50	POLR2A	chr9:96213111-96216260	GM18526	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:95708784..95711358-chr9:96213029..96214881,2	K562	blood:
2	chr5:140699114..140701458-chr9:96212553..96215118,2	MCF-7	breast:
3	chr9:96212024..96217170-chr9:96326121..96330116,7	MCF-7	breast:
4	chr9:96211528..96214948-chr9:96337573..96343441,10	MCF-7	breast:
5	chr9:95431480..95432991-chr9:96212383..96214894,2	MCF-7	breast:
6	chr9:96069590..96071864-chr9:96210674..96213644,2	MCF-7	breast:
7	chr9:96210381..96218248-chr9:96327402..96333234,10	MCF-7	breast:
8	chr9:95857571..95862229-chr9:96211597..96216359,5	K562	blood:
9	chr9:96196696..96199442-chr9:96211213..96213936,2	K562	blood:
10	chr9:96212967..96214736-chr9:96291128..96293396,2	MCF-7	breast:
11	chr9:96211603..96213302-chr9:96293389..96295575,2	MCF-7	breast:
12	chr11:843529..844337-chr9:96213113..96213884,2	Hela-S3	cervix:
13	chr17:57917246..57919859-chr9:96211459..96213785,2	MCF-7	breast:
14	chr9:95856800..95859803-chr9:96212504..96215667,3	MCF-7	breast:
15	chr9:91925154..91927939-chr9:96212965..96214710,2	K562	blood:
16	chr9:95820491..95823416-chr9:96211285..96213612,2	K562	blood:
17	chr9:96072987..96083429-chr9:96209751..96218385,15	MCF-7	breast:
18	chr9:96176371..96177896-chr9:96210682..96213241,2	MCF-7	breast:
19	chr1:145382535..145383246-chr9:96213034..96214021,2	Hela-S3	cervix:
20	chr1:209720785..209723139-chr9:96211827..96213695,2	MCF-7	breast:
21	chr9:95893830..95897202-chr9:96212872..96217148,4	MCF-7	breast:
22	chr9:96211672..96218862-chr9:96335264..96341672,16	MCF-7	breast:
23	chr8:91656166..91658679-chr9:96213011..96215220,2	MCF-7	breast:
24	chr19:35490178..35491130-chr9:96213088..96214069,2	Hela-S3	cervix:

Variant related genes	Relation type
FAM120A	TF binding region
ENSG00000227603	Chromatin interaction
ENSG00000165238	Chromatin interaction
ENSG00000127084	Chromatin interaction
ENSG00000269303	Chromatin interaction
ENSG00000255729	Chromatin interaction
ENSG00000246792	Chromatin interaction
ENSG00000223446	Chromatin interaction
ENSG00000197724	Chromatin interaction
ENSG00000224260	Chromatin interaction
ENSG00000201558	Chromatin interaction
ENSG00000123975	Chromatin interaction
ENSG00000165233	Chromatin interaction
ENSG00000048828	Chromatin interaction
ENSG00000127080	Chromatin interaction
ENSG00000157303	Chromatin interaction
ENSG00000199004	Chromatin interaction
ENSG00000263875	Chromatin interaction
ENSG00000131669	Chromatin interaction
ENSG00000214063	Chromatin interaction
ENSG00000089351	Chromatin interaction
ENSG00000265112	Chromatin interaction
ENSG00000178913	Chromatin interaction
ENSG00000180694	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10429558	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs11975	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs12335532	0.91[CEU][hapmap]
rs12341488	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs12554020	0.91[CEU][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3933797	0.91[CEU][hapmap]
rs4552973	0.91[CEU][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59483310	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs59582399	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6479482	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479483	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6479487	0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6479494	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs7020459	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7023933	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7025805	0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7028729	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7035657	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7036984	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7048853	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7850322	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7853605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7857183	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs7859267	0.90[CEU][hapmap];0.88[CHB][hapmap]
rs7860098	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7862998	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7874126	0.82[YRI][hapmap]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3815563	RP11-165J3.6	cis	Skin Sun Exposed Lower leg	GTEx
rs3815563	RP11-165J3.6	cis	Esophagus Muscularis	GTEx
rs3815563	RP11-165J3.6	cis	Nerve Tibial	GTEx
rs3815563	RP11-165J3.6	cis	Artery Tibial	GTEx
rs3815563	FAM120AOS	Cis_1M	lymphoblastoid	RTeQTL
rs3815563	RP11-165J3.6	cis	Thyroid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96212000-96213600	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr9:96212200-96213200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr9:96212200-96213200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
4	chr9:96212200-96213600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr9:96212200-96216200	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr9:96212400-96213200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr9:96212400-96213200	Flanking Active TSS	Brain Anterior Caudate	brain
8	chr9:96212400-96213200	Flanking Active TSS	Stomach Smooth Muscle	stomach
9	chr9:96212400-96213400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr9:96212400-96213400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr9:96212400-96213400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr9:96212400-96213400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr9:96212400-96213400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr9:96212400-96213600	Flanking Active TSS	Primary T cells from cord blood	blood
15	chr9:96212400-96213600	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
16	chr9:96212400-96216000	Active TSS	NHLF	lung
17	chr9:96212400-96216200	Active TSS	Fetal Kidney	kidney
18	chr9:96212400-96216400	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr9:96212400-96216400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr9:96212400-96216400	Active TSS	A549	lung
21	chr9:96212400-96216400	Active TSS	HSMM	muscle
22	chr9:96212400-96216600	Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr9:96212400-96216800	Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr9:96212400-96216800	Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr9:96212400-96217000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr9:96212400-96217000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr9:96212600-96213200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr9:96212600-96213200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
29	chr9:96212600-96213200	Flanking Active TSS	Primary B cells from peripheral blood	blood
30	chr9:96212600-96213200	Flanking Active TSS	Primary hematopoietic stem cells	blood
31	chr9:96212600-96213200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
32	chr9:96212600-96213200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
33	chr9:96212600-96213200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
34	chr9:96212600-96213200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
35	chr9:96212600-96213200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr9:96212600-96213200	Flanking Active TSS	Liver	Liver
37	chr9:96212600-96213200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
38	chr9:96212600-96213200	Flanking Active TSS	Brain Substantia Nigra	brain
39	chr9:96212600-96213200	Flanking Active TSS	Fetal Thymus	thymus
40	chr9:96212600-96213200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
41	chr9:96212600-96213200	Flanking Active TSS	Osteobl	bone
42	chr9:96212600-96213400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr9:96212600-96213400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
44	chr9:96212600-96213400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
45	chr9:96212600-96213400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
46	chr9:96212600-96213400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr9:96212600-96213400	Flanking Active TSS	Adipose Nuclei	Adipose
48	chr9:96212600-96213400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
49	chr9:96212600-96213400	Flanking Active TSS	Fetal Muscle Leg	muscle
50	chr9:96212600-96213400	Active TSS	Right Atrium	heart

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