Variant report

Variant	rs752848
Chromosome Location	chr11:47175176-47175177
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	CTCF	chr11:47173779-47175556	SK-N-SH	brain:	n/a	chr11:47174815-47174836 chr11:47174822-47174835 chr11:47174820-47174838 chr11:47173836-47173844 chr11:47174821-47174837
2	RAD21	chr11:47174569-47175176	A549	lung:	n/a	chr11:47174818-47174837 chr11:47174697-47174709 chr11:47174822-47174836 chr11:47174824-47174833
3	CTCF	chr11:47174015-47175271	A549	lung:	n/a	chr11:47174815-47174836 chr11:47174822-47174835 chr11:47174820-47174838 chr11:47174821-47174837
4	RAD21	chr11:47173739-47175488	SK-N-SH	brain:	n/a	chr11:47174818-47174837 chr11:47174697-47174709 chr11:47174822-47174836 chr11:47174824-47174833
5	RAD21	chr11:47174458-47175328	HCT-116	colon:	n/a	chr11:47174818-47174837 chr11:47174697-47174709 chr11:47174822-47174836 chr11:47174824-47174833
6	POLR2A	chr11:47173928-47175390	HepG2	liver:	n/a	n/a
7	CTCF	chr11:47174435-47175256	HCT-116	colon:	n/a	chr11:47174815-47174836 chr11:47174822-47174835 chr11:47174820-47174838 chr11:47174821-47174837
8	RAD21	chr11:47174447-47175187	ECC-1	luminal epithelium:	n/a	chr11:47174818-47174837 chr11:47174697-47174709 chr11:47174822-47174836 chr11:47174824-47174833
9	POLR2A	chr11:47174325-47175285	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr11:47173818-47175361	Hela-S3	cervix:	n/a	n/a
11	CTCF	chr11:47175160-47175310	GM12872	blood:	n/a	n/a
12	RAD21	chr11:47174377-47175182	MCF-7	breast:	n/a	chr11:47174818-47174837 chr11:47174697-47174709 chr11:47174822-47174836 chr11:47174824-47174833
13	CTCF	chr11:47175100-47175250	GM12869	blood:	n/a	n/a
14	CTCF	chr11:47174456-47175179	MCF-7	breast:	n/a	chr11:47174815-47174836 chr11:47174822-47174835 chr11:47174820-47174838 chr11:47174821-47174837
15	RAD21	chr11:47174384-47175205	HCT-116	colon:	n/a	chr11:47174818-47174837 chr11:47174697-47174709 chr11:47174822-47174836 chr11:47174824-47174833
16	CTCF	chr11:47175160-47175310	GM12873	blood:	n/a	n/a
17	SMC3	chr11:47174207-47175551	SK-N-SH	brain:	n/a	chr11:47174380-47174388 chr11:47174822-47174836 chr11:47174557-47174564
18	CTCF	chr11:47175140-47175290	HCT-116	colon:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:47175143-47175193	PFSK-1	brain:	n/a
2	chr11:47175143-47175193	HCPEpiC	choroid plexus:	n/a
3	chr11:47175143-47175193	BJ	skin:	n/a
4	chr11:47175143-47175193	HEEpiC	esophagus:	n/a
5	chr11:47175143-47175193	Caco-2	colon:	n/a
6	chr11:47175143-47175193	SKMC	muscle:	n/a
7	chr11:47175143-47175193	GM12878	blood:	n/a
8	chr11:47175143-47175193	GM12891	blood:	n/a
9	chr11:47175143-47175193	NHBE	bronchial:	n/a
10	chr11:47175143-47175193	ovcar-3	ovarian:	n/a
11	chr11:47175143-47175193	LNCaP	prostate:	n/a
12	chr11:47175143-47175193	Hepatocyte	liver:	n/a
13	chr11:47175143-47175193	RPTEC	kidney:	n/a
14	chr11:47175143-47175193	HAEpiC	amniotic membrane:	n/a
15	chr11:47175143-47175193	SAEC	small airway:	n/a
16	chr11:47175143-47175193	AG09309	skin:	n/a
17	chr11:47175143-47175193	HCT-116	colon:	n/a
18	chr11:47175143-47175193	T-47D	breast:	n/a
19	chr11:47175143-47175193	BE2_C	brain:	n/a
20	chr11:47175143-47175193	HPAEpiC	pulmonary alveolar:	n/a
21	chr11:47175143-47175193	HRE	kidney:	n/a
22	chr11:47175143-47175193	HMEC	breast:	n/a
23	chr11:47175143-47175193	HCM	heart:	n/a
24	chr11:47175143-47175193	AG09319	gingival:	n/a
25	chr11:47175143-47175193	Jurkat	blood:	n/a
26	chr11:47175143-47175193	SK-N-MC	brain:	n/a
27	chr11:47175143-47175193	HepG2	liver:	n/a
28	chr11:47175143-47175193	MCF-7	breast:	n/a
29	chr11:47175143-47175193	NH-A	brain:	n/a
30	chr11:47175143-47175193	HL-60	blood:	n/a
31	chr11:47175143-47175193	AoSMC	blood vessel:	n/a
32	chr11:47175143-47175193	U87	brain:	n/a
33	chr11:47175143-47175193	NT2-D1	testis:	n/a
34	chr11:47175143-47175193	GM19239	blood:	n/a
35	chr11:47175143-47175193	PANC-1	pancreas:	n/a
36	chr11:47175143-47175193	AG10803	skin:	n/a
37	chr11:47175143-47175193	SK-N-SH	brain:	n/a
38	chr11:47175143-47175193	Hela-S3	cervix:	n/a
39	chr11:47175143-47175193	GM12892	blood:	n/a
40	chr11:47175143-47175193	CMK	blood:	n/a
41	chr11:47175143-47175193	SK-N-SH_RA	brain:	n/a
42	chr11:47175143-47175193	PrEC	prostate:	n/a
43	chr11:47175143-47175193	ProgFib	skin:	n/a
44	chr11:47175143-47175193	AG04450	lung:	fetal
45	chr11:47175143-47175193	NHDF-neo	bronchial:	n/a
46	chr11:47175143-47175193	AG04449	skin:	fetal
47	chr11:47175143-47175193	NB4	blood:	n/a
48	chr11:47175143-47175193	HRPEpiC	eye:	n/a
49	chr11:47175143-47175193	HEK293	kidney:	embryo
50	chr11:47175143-47175193	ECC-1	luminal epithelium:	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:46867413..46869550-chr11:47174916..47176891,2	K562	blood:
2	chr11:46941180..46942052-chr11:47174287..47175251,5	K562	blood:
3	chr11:47173854..47175804-chr11:47178111..47180557,3	K562	blood:
4	chr11:47174382..47175264-chr11:47376452..47377398,3	K562	blood:
5	chr11:46941286..46942092-chr11:47174349..47175242,5	MCF-7	breast:
6	chr11:46910320..46911827-chr11:47174259..47175968,19	MCF-7	breast:
7	chr11:46910929..46911796-chr11:47174261..47175544,7	MCF-7	breast:
8	chr11:47008492..47009359-chr11:47174486..47175315,3	MCF-7	breast:
9	chr11:47174410..47175370-chr11:47376484..47377024,2	MCF-7	breast:
10	chr11:46958122..46959949-chr11:47174429..47176046,2	MCF-7	breast:
11	chr11:47174366..47175306-chr11:47280943..47281453,2	MCF-7	breast:
12	chr11:46910425..46912611-chr11:47175096..47177749,2	K562	blood:
13	chr11:46910841..46911860-chr11:47174311..47175319,17	K562	blood:

Variant related genes	Relation type
C11orf49	TF binding region
C11orf49	CpG island
ENSG00000247675	Chromatin interaction
ENSG00000175216	Chromatin interaction
ENSG00000149179	Chromatin interaction
ENSG00000025434	Chromatin interaction
ENSG00000134569	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11039076	0.83[ASN][1000 genomes]
rs11039122	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11039131	0.84[AFR][1000 genomes]
rs11570094	1.00[YRI][hapmap]
rs12365578	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12796744	1.00[YRI][hapmap]
rs12803718	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1685404	0.84[CHB][hapmap]
rs17787966	0.96[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs2291119	1.00[YRI][hapmap]
rs2291443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2856650	1.00[YRI][hapmap]
rs3740690	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs752850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7946709	1.00[YRI][hapmap]
rs901750	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs752848	LRP4	cis	Nerve Tibial	GTEx
rs752848	C1QTNF4	cis	multi-tissue	Pritchard
rs752848	CTD-2384B9.1	cis	Nerve Tibial	GTEx
rs752848	LRP4-AS1	cis	Nerve Tibial	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47143600-47175200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr11:47160000-47176400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr11:47161600-47176000	Weak transcription	Dnd41	blood
4	chr11:47165000-47184800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr11:47165000-47185000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr11:47165200-47185600	Weak transcription	Aorta	Aorta
7	chr11:47165400-47177600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr11:47165400-47188600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr11:47165600-47177600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr11:47165600-47177800	Weak transcription	NHEK	skin
11	chr11:47168600-47177800	Weak transcription	A549	lung
12	chr11:47169200-47176000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr11:47170800-47176800	Weak transcription	Lung	lung
14	chr11:47171000-47175200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr11:47171000-47177200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr11:47171000-47177600	Weak transcription	Esophagus	oesophagus
17	chr11:47171000-47183400	Weak transcription	Gastric	stomach
18	chr11:47171200-47176000	Weak transcription	Fetal Brain Female	brain
19	chr11:47171200-47177600	Weak transcription	Ovary	ovary
20	chr11:47171400-47186000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr11:47171600-47186400	Weak transcription	Psoas Muscle	Psoas
22	chr11:47173800-47175200	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr11:47173800-47175400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr11:47173800-47175400	Enhancers	Brain Hippocampus Middle	brain
25	chr11:47173800-47175400	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr11:47173800-47175600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr11:47173800-47175600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr11:47173800-47176000	Enhancers	Rectal Mucosa Donor 29	rectum
29	chr11:47173800-47176400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr11:47173800-47176800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr11:47173800-47177000	Enhancers	Fetal Muscle Trunk	muscle
32	chr11:47173800-47178000	Enhancers	Fetal Thymus	thymus
33	chr11:47174000-47175200	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr11:47174000-47175200	Enhancers	Brain Substantia Nigra	brain
35	chr11:47174000-47175200	Enhancers	Fetal Intestine Large	intestine
36	chr11:47174000-47175200	Enhancers	Placenta	Placenta
37	chr11:47174000-47175200	Genic enhancers	Fetal Stomach	stomach
38	chr11:47174000-47175400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr11:47174000-47175400	Enhancers	Fetal Intestine Small	intestine
40	chr11:47174000-47175400	Enhancers	Pancreas	Pancrea
41	chr11:47174000-47175600	Enhancers	NHDF-Ad	bronchial
42	chr11:47174000-47176000	Enhancers	Primary T cells from cord blood	blood
43	chr11:47174000-47176000	Enhancers	Fetal Muscle Leg	muscle
44	chr11:47174000-47176600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr11:47174000-47176600	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr11:47174000-47176800	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr11:47174000-47176800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr11:47174000-47178000	Enhancers	Primary T cells fromperipheralblood	blood
49	chr11:47174200-47175200	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr11:47174200-47175200	Enhancers	Fetal Lung	lung

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