Variant report

Variant	rs503156
Chromosome Location	chr11:65820673-65820674
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:65820508-65821039	HepG2	liver:	n/a	n/a
2	REST	chr11:65818427-65820727	H1-neurons	neurons:	n/a	chr11:65819271-65819284
3	POLR2A	chr11:65820622-65820711	ProgFib	skin:	n/a	n/a
4	HCFC1	chr11:65818081-65820872	Hela-S3	cervix:	n/a	n/a
5	MXI1	chr11:65819040-65820911	IMR90	lung:	n/a	n/a
6	SIN3AK20	chr11:65818889-65820728	MCF-7	breast:	n/a	n/a
7	STAT5A	chr11:65820223-65820924	GM12878	blood:	n/a	n/a
8	WRNIP1	chr11:65819764-65820889	GM12878	blood:	n/a	n/a
9	POLR2A	chr11:65819053-65820701	K562	blood:	n/a	n/a
10	MAFK	chr11:65820536-65820692	HepG2	liver:	n/a	n/a
11	MAZ	chr11:65818871-65820883	IMR90	lung:	n/a	chr11:65819555-65819565
12	CTCF	chr11:65820620-65820770	GM12872	blood:	n/a	n/a

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65816864..65823380-chr11:65832037..65840391,16	MCF-7	breast:
2	chr11:65486463..65488167-chr11:65819267..65821152,2	K562	blood:
3	chr11:65778958..65780961-chr11:65818944..65820828,4	MCF-7	breast:
4	chr11:65625573..65627850-chr11:65819625..65821222,2	MCF-7	breast:
5	chr11:65812475..65816551-chr11:65816982..65820716,11	MCF-7	breast:
6	chr11:65767679..65771369-chr11:65818165..65822112,6	MCF-7	breast:
7	chr11:65766270..65769793-chr11:65817988..65822487,7	MCF-7	breast:
8	chr11:65788326..65791572-chr11:65817870..65821514,6	MCF-7	breast:
9	chr11:65624197..65629461-chr11:65817994..65821738,6	K562	blood:
10	chr11:65727969..65730897-chr11:65818847..65821349,3	MCF-7	breast:
11	chr11:65727674..65729529-chr11:65819509..65821064,2	K562	blood:
12	chr11:65666594..65669601-chr11:65818513..65821111,3	K562	blood:
13	chr11:65768250..65771590-chr11:65817294..65821421,6	K562	blood:
14	chr11:65624171..65627161-chr11:65818449..65820914,2	K562	blood:
15	chr11:65819217..65821138-chr15:96872080..96874468,2	MCF-7	breast:
16	chr11:65811021..65815121-chr11:65816503..65821449,7	K562	blood:
17	chr11:65429132..65431872-chr11:65817636..65822281,4	MCF-7	breast:
18	chr11:65768250..65771110-chr11:65819143..65821313,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PACS1-1	chr11:65820615-65820699	ENSG00000255013.1

No data

Variant related genes	Relation type
SF3B2	TF binding region
GAL3ST3	TF binding region
ENSG00000175229	Chromatin interaction
ENSG00000175294	Chromatin interaction
ENSG00000175592	Chromatin interaction
ENSG00000087365	Chromatin interaction
ENSG00000185551	Chromatin interaction
ENSG00000173039	Chromatin interaction
ENSG00000172922	Chromatin interaction
ENSG00000175334	Chromatin interaction
ENSG00000175376	Chromatin interaction
ENSG00000172757	Chromatin interaction
ENSG00000175467	Chromatin interaction
ENSG00000255038	Chromatin interaction
ENSG00000175315	Chromatin interaction
ENSG00000175115	Chromatin interaction
ENSG00000172732	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1049872	0.84[EUR][1000 genomes]
rs1203998	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.81[LWK][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12803276	0.84[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs17147371	0.84[MEX][hapmap]
rs2000672	0.83[EUR][1000 genomes]
rs2452680	0.88[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs2576	0.80[MEX][hapmap]
rs33988687	0.84[EUR][1000 genomes]
rs34073119	0.83[EUR][1000 genomes]
rs34123790	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35611816	0.98[EUR][1000 genomes]
rs477280	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs491618	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs535752	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs547404	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs557799	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs570887	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs574153	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7480811	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs873491	0.84[MEX][hapmap]
rs947847	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948711	chr11:65692760-65949674	Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
2	nsv897768	chr11:65715210-65842064	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
3	nsv897769	chr11:65727799-65828625	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
4	esv3335923	chr11:65741698-66175759	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
5	esv1819302	chr11:65787660-66007018	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers 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	43 gene(s)	inside rSNPs	diseases
6	esv3407551	chr11:65794503-66158322	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv897770	chr11:65803750-65824472	Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs503156	SF3B2	cis	cerebellum	SCAN
rs503156	SF3B2	cis	parietal	SCAN
rs503156	SLC22A6	cis	cerebellum	SCAN
rs503156	SF3B2	cis	Whole Blood	GTEx
rs503156	SF3B2	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65818800-65820800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr11:65818800-65821000	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr11:65818800-65821000	Active TSS	H9 Cell Line	embryonic stem cell
4	chr11:65819000-65820800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr11:65819000-65820800	Active TSS	Aorta	Aorta
6	chr11:65819000-65820800	Active TSS	Right Atrium	heart
7	chr11:65819000-65821000	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr11:65819200-65820800	Active TSS	NHDF-Ad	bronchial
9	chr11:65819400-65820800	Active TSS	HMEC	breast
10	chr11:65819800-65821200	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
11	chr11:65819800-65821200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
12	chr11:65820000-65820800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
13	chr11:65820000-65820800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
14	chr11:65820000-65820800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
15	chr11:65820000-65820800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
16	chr11:65820000-65820800	Bivalent/Poised TSS	HepG2	liver
17	chr11:65820000-65821000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
18	chr11:65820000-65821000	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr11:65820000-65821000	Flanking Active TSS	Primary hematopoietic stem cells	blood
20	chr11:65820000-65821000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr11:65820000-65821000	Flanking Active TSS	Adipose Nuclei	Adipose
22	chr11:65820000-65821000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
23	chr11:65820000-65821000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr11:65820000-65821200	Flanking Active TSS	Stomach Smooth Muscle	stomach
25	chr11:65820000-65821200	Transcr. at gene 5' and 3'	Dnd41	blood
26	chr11:65820200-65820800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
27	chr11:65820200-65820800	Flanking Active TSS	Primary B cells from peripheral blood	blood
28	chr11:65820200-65820800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
29	chr11:65820200-65821000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
30	chr11:65820200-65821000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr11:65820200-65821000	Flanking Active TSS	Liver	Liver
32	chr11:65820200-65821000	Flanking Active TSS	Brain Angular Gyrus	brain
33	chr11:65820200-65821000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
34	chr11:65820200-65821000	Flanking Active TSS	Fetal Muscle Trunk	muscle
35	chr11:65820200-65821000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
36	chr11:65820200-65821200	Flanking Active TSS	Primary T cells from cord blood	blood
37	chr11:65820200-65821200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
38	chr11:65820400-65820800	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr11:65820400-65820800	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr11:65820400-65820800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
41	chr11:65820400-65820800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
42	chr11:65820400-65820800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr11:65820400-65820800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr11:65820400-65820800	Flanking Active TSS	Fetal Brain Male	brain
45	chr11:65820400-65820800	Flanking Active TSS	Fetal Heart	heart
46	chr11:65820400-65820800	Flanking Active TSS	Placenta	Placenta
47	chr11:65820400-65820800	Flanking Active TSS	Placenta Amnion	Placenta Amnion
48	chr11:65820400-65820800	Flanking Active TSS	Spleen	Spleen
49	chr11:65820400-65821000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr11:65820400-65821000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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