Variant report

Variant	rs947799
Chromosome Location	chr11:64851305-64851306
allele	C/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	SIN3AK20	chr11:64851171-64852143	SK-N-SH	brain:	n/a	n/a
2	CTCF	chr11:64851220-64851370	HCPEpiC	choroid plexus:	n/a	n/a
3	CTCF	chr11:64851180-64851330	GM12872	blood:	n/a	n/a
4	REST	chr11:64851006-64851877	A549	lung:	n/a	n/a
5	POLR2A	chr11:64851252-64851945	Gliobla	brain:	n/a	n/a
6	CBX3	chr11:64851165-64851805	K562	blood:	n/a	n/a
7	ETS1	chr11:64851226-64851874	K562	blood:	n/a	chr11:64851562-64851572 chr11:64851561-64851570 chr11:64851773-64851784 chr11:64851758-64851771
8	YY1	chr11:64850970-64852049	SK-N-SH	brain:	n/a	chr11:64851903-64851912 chr11:64851634-64851645
9	SP1	chr11:64851253-64852052	A549	lung:	n/a	chr11:64851951-64851963 chr11:64851642-64851652 chr11:64851878-64851888 chr11:64851952-64851961 chr11:64851903-64851913 chr11:64851903-64851912 chr11:64851904-64851913 chr11:64851951-64851963 chr11:64851903-64851913 chr11:64851874-64851888 chr11:64851877-64851889 chr11:64851902-64851914 chr11:64851878-64851888 chr11:64851861-64851873 chr11:64851904-64851913 chr11:64851861-64851873 chr11:64851879-64851888 chr11:64851877-64851889 chr11:64851899-64851913 chr11:64851902-64851914 chr11:64851863-64851872 chr11:64851878-64851887
10	POLR2A	chr11:64851292-64851866	GM12892	blood:	n/a	n/a
11	MYC	chr11:64851180-64851870	K562	blood:	n/a	n/a
12	POLR2A	chr11:64850781-64852339	HUVEC	blood vessel:	n/a	n/a
13	E2F4	chr11:64851104-64852117	K562	blood:	n/a	chr11:64851903-64851912
14	YY1	chr11:64851034-64851882	GM12878	blood:	n/a	chr11:64851634-64851645
15	TEAD4	chr11:64851131-64851795	K562	blood:	n/a	n/a
16	SIN3AK20	chr11:64851286-64851955	A549	lung:	n/a	n/a
17	GABPA	chr11:64851192-64851882	Hela-S3	cervix:	n/a	chr11:64851560-64851567
18	POLR2A	chr11:64851173-64852109	Hela-S3	cervix:	n/a	n/a
19	SRF	chr11:64851079-64852143	HCT-116	colon:	n/a	n/a
20	E2F4	chr11:64850137-64852053	MCF10A-Er-Src	breast:	n/a	chr11:64851903-64851912
21	SIX5	chr11:64850736-64852013	A549	lung:	n/a	n/a
22	ELK1	chr11:64851145-64851872	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr11:64850851-64852124	GM19099	blood:	n/a	n/a
24	TAF1	chr11:64851227-64851991	ECC-1	luminal epithelium:	n/a	n/a
25	POLR2A	chr11:64851199-64851912	ECC-1	luminal epithelium:	n/a	n/a
26	POLR2A	chr11:64851251-64852386	SK-N-MC	brain:	n/a	n/a
27	POLR2A	chr11:64851207-64852124	K562	blood:	n/a	n/a
28	MXI1	chr11:64851226-64851866	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr11:64851137-64851876	PBDE	blood:	n/a	n/a
30	POLR2A	chr11:64850692-64852163	Hela-S3	cervix:	n/a	n/a
31	EP300	chr11:64851176-64851858	A549	lung:	n/a	n/a
32	POLR2A	chr11:64851287-64852097	GM18526	blood:	n/a	n/a
33	POLR2A	chr11:64851300-64852193	HepG2	liver:	n/a	n/a
34	POLR2A	chr11:64851258-64852151	SK-N-SH	brain:	n/a	n/a
35	POLR2A	chr11:64851242-64852173	Raji	blood:	n/a	n/a
36	ZNF263	chr11:64850918-64851710	HEK293-T-REx	kidney:	n/a	chr11:64851072-64851081
37	SIN3A	chr11:64850900-64852313	H1-hESC	embryonic stem cell:	n/a	chr11:64851942-64851955
38	YY1	chr11:64851236-64851851	SK-N-SH_RA	brain:	n/a	chr11:64851634-64851645
39	POLR2A	chr11:64850812-64852226	HL-60	blood:	n/a	n/a
40	CTCF	chr11:64851240-64851390	HFF-Myc	foreskin:	n/a	n/a
41	POLR2A	chr11:64850621-64852316	K562	blood:	n/a	n/a
42	POLR2A	chr11:64850794-64852245	U87	brain:	n/a	n/a
43	POLR2A	chr11:64850144-64853317	K562	blood:	n/a	n/a
44	POLR2A	chr11:64851292-64852108	ProgFib	skin:	n/a	n/a
45	POLR2A	chr11:64851235-64852017	MCF-7	breast:	n/a	n/a
46	GABPA	chr11:64850653-64851916	A549	lung:	n/a	chr11:64851903-64851912 chr11:64851560-64851567
47	CREB1	chr11:64851088-64852112	GM12878	blood:	n/a	chr11:64851662-64851675
48	YY1	chr11:64851118-64851844	SK-N-SH_RA	brain:	n/a	chr11:64851634-64851645
49	RELA	chr11:64851240-64851923	GM15510	blood:	n/a	n/a
50	CTCF	chr11:64851280-64851430	GM12873	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:64849716..64853170-chr11:64935136..64939292,4	K562	blood:
2	chr11:64779637..64784611-chr11:64849890..64854060,9	K562	blood:
3	chr11:64851267..64851847-chrX:53448899..53449422,2	Hela-S3	cervix:
4	chr11:64849453..64851884-chr11:64947314..64948879,2	K562	blood:
5	chr11:64781269..64783468-chr11:64850067..64853147,4	MCF-7	breast:
6	chr11:64825921..64828072-chr11:64849835..64851535,2	K562	blood:
7	chr11:64807090..64809871-chr11:64850334..64853304,4	MCF-7	breast:
8	chr11:64849359..64854600-chr11:64874292..64883144,16	MCF-7	breast:
9	chr11:64779668..64784219-chr11:64849890..64854919,7	K562	blood:
10	chr11:64807684..64812709-chr11:64850593..64853492,4	MCF-7	breast:
11	chr11:64544180..64546675-chr11:64850197..64851760,2	MCF-7	breast:
12	chr11:64849716..64856389-chr11:64935136..64940419,9	K562	blood:
13	chr11:64644760..64647431-chr11:64850066..64853139,4	K562	blood:
14	chr11:64804480..64810811-chr11:64850224..64856247,12	K562	blood:
15	chr11:64849686..64855071-chr11:64883547..64886732,9	MCF-7	breast:
16	chr11:64794878..64795449-chr11:64851133..64851640,2	NB4	blood:
17	chr11:64849456..64854518-chr11:64877116..64882654,9	K562	blood:
18	chr11:64807098..64808802-chr11:64850233..64851800,2	K562	blood:
19	chr11:64849186..64851415-chr11:65269391..65271691,2	K562	blood:
20	chr11:64793687..64796323-chr11:64849331..64852233,3	K562	blood:
21	chr11:64850072..64852972-chr11:65026497..65029318,2	K562	blood:
22	chr11:64644462..64647222-chr11:64847025..64851524,4	MCF-7	breast:
23	chr11:64643788..64647961-chr11:64848883..64851896,4	K562	blood:
24	chr11:64793181..64796302-chr11:64849635..64852378,4	MCF-7	breast:
25	chr11:64793383..64797474-chr11:64849331..64856424,6	K562	blood:
26	chr11:64850973..64853282-chr11:65265136..65266781,2	K562	blood:
27	chr11:64832671..64835759-chr11:64851097..64853512,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AP003068.6.1-2	chr11:64851101-64851368	NONHSAT022067

Variant related genes	Relation type
ZFPL1	TF binding region
CDCA5	TF binding region
ENSG00000213465	Chromatin interaction
ENSG00000149823	Chromatin interaction
ENSG00000251562	Chromatin interaction
ENSG00000168066	Chromatin interaction
ENSG00000072501	Chromatin interaction
ENSG00000168061	Chromatin interaction
ENSG00000204710	Chromatin interaction
ENSG00000168060	Chromatin interaction
ENSG00000174276	Chromatin interaction
ENSG00000146670	Chromatin interaction
ENSG00000270117	Chromatin interaction
ENSG00000254614	Chromatin interaction
ENSG00000014216	Chromatin interaction
ENSG00000149809	Chromatin interaction
ENSG00000273003	Chromatin interaction
ENSG00000255173	Chromatin interaction
ENSG00000270775	Chromatin interaction
ENSG00000014138	Chromatin interaction
ENSG00000110025	Chromatin interaction
ENSG00000110047	Chromatin interaction
ENSG00000254501	Chromatin interaction
ENSG00000269038	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10791813	0.82[ASN][1000 genomes]
rs11227118	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11227120	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11231929	0.92[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap]
rs1129195	0.84[CHB][hapmap]
rs1196048	0.92[CEU][hapmap];0.82[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1300845	0.80[CEU][hapmap];0.89[CHB][hapmap]
rs2282498	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2282499	0.84[CHB][hapmap]
rs2507814	0.80[CHB][hapmap];0.83[JPT][hapmap]
rs36057475	0.80[ASN][1000 genomes]
rs3759041	0.80[CEU][hapmap]
rs3782094	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3802936	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3862374	0.92[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap]
rs475089	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs477539	0.92[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap]
rs484182	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs486984	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs488686	0.80[CEU][hapmap];0.89[CHB][hapmap]
rs489489	0.92[CEU][hapmap];0.82[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs496427	0.90[EUR][1000 genomes]
rs502333	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs532373	0.88[CEU][hapmap]
rs534236	0.81[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs548150	0.92[CEU][hapmap];0.82[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes]
rs562590	0.84[CHB][hapmap]
rs564966	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs566221	0.80[CEU][hapmap];0.89[CHB][hapmap]
rs653111	0.92[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs6591869	0.88[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs7123226	0.88[ASN][1000 genomes]
rs7130183	0.97[ASN][1000 genomes]
rs7943007	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs9971546	0.82[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526181	chr11:64638041-65257329	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1539 gene(s)	inside rSNPs	diseases
2	nsv897709	chr11:64772545-64870779	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv897710	chr11:64772545-64885445	Flanking Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
4	nsv897711	chr11:64772545-64900270	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs947799	SPDYC	cis	parietal	SCAN
rs947799	SNX15	cis	lymphoblastoid	seeQTL
rs947799	SCGB2A2	cis	cerebellum	SCAN
rs947799	TM7SF2	cis	cerebellum	SCAN
rs947799	SNX15	cis	Muscle Skeletal	GTEx
rs947799	SNX15	cis	parietal	SCAN
rs947799	RAB1B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64850200-64851400	Flanking Active TSS	Brain Germinal Matrix	brain
2	chr11:64850200-64852800	Active TSS	H9 Cell Line	embryonic stem cell
3	chr11:64850400-64851400	Flanking Active TSS	Primary hematopoietic stem cells	blood
4	chr11:64850400-64851400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr11:64850400-64851400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr11:64850400-64851400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
7	chr11:64850400-64851400	Flanking Active TSS	Fetal Thymus	thymus
8	chr11:64850400-64852600	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr11:64850600-64851400	Flanking Active TSS	Duodenum Mucosa	Duodenum
10	chr11:64850600-64851400	Flanking Active TSS	Fetal Brain Female	brain
11	chr11:64850600-64851400	Flanking Active TSS	Fetal Lung	lung
12	chr11:64850600-64851400	Flanking Active TSS	Fetal Muscle Leg	muscle
13	chr11:64850600-64851400	Flanking Active TSS	Fetal Stomach	stomach
14	chr11:64850600-64851400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
15	chr11:64850600-64851400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr11:64850600-64851600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr11:64850600-64851600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
18	chr11:64850600-64851600	Flanking Active TSS	Placenta	Placenta
19	chr11:64850600-64852000	Active TSS	Rectal Smooth Muscle	rectum
20	chr11:64850600-64852400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr11:64850600-64852400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr11:64850600-64852400	Active TSS	A549	lung
23	chr11:64850600-64852800	Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr11:64850800-64851400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr11:64850800-64851400	Flanking Active TSS	Primary T cells from cord blood	blood
26	chr11:64850800-64851400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr11:64850800-64851400	Flanking Active TSS	Colonic Mucosa	Colon
28	chr11:64850800-64851400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr11:64850800-64851400	Flanking Active TSS	Fetal Brain Male	brain
30	chr11:64850800-64851400	Flanking Active TSS	Fetal Muscle Trunk	muscle
31	chr11:64850800-64851400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
32	chr11:64850800-64851400	Enhancers	Stomach Mucosa	stomach
33	chr11:64850800-64851600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
34	chr11:64850800-64851600	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr11:64850800-64851600	Flanking Active TSS	Stomach Smooth Muscle	stomach
36	chr11:64850800-64852000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr11:64850800-64852200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr11:64850800-64852400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
39	chr11:64850800-64852400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr11:64850800-64852400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr11:64850800-64852400	Active TSS	iPS-20b Cell Line	embryonic stem cell
42	chr11:64850800-64852400	Active TSS	Fetal Kidney	kidney
43	chr11:64850800-64852400	Bivalent/Poised TSS	HepG2	liver
44	chr11:64850800-64852400	Active TSS	K562	blood
45	chr11:64850800-64852600	Active TSS	ES-I3 Cell Line	embryonic stem cell
46	chr11:64850800-64852600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr11:64850800-64852600	Active TSS	HUES48 Cell Line	embryonic stem cell
48	chr11:64850800-64852800	Active TSS	iPS-15b Cell Line	embryonic stem cell
49	chr11:64850800-64853000	Active TSS	H1 Cell Line	embryonic stem cell
50	chr11:64850800-64853000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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