Variant report

Variant	rs575134
Chromosome Location	chr11:62461229-62461230
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr11:62460945-62461372	ECC-1	luminal epithelium:	n/a	n/a
2	USF1	chr11:62460952-62461326	ECC-1	luminal epithelium:	n/a	n/a
3	NFIC	chr11:62460927-62461603	ECC-1	luminal epithelium:	n/a	n/a
4	TEAD4	chr11:62461030-62461410	ECC-1	luminal epithelium:	n/a	n/a
5	MAX	chr11:62461084-62461378	ECC-1	luminal epithelium:	n/a	n/a
6	NFIC	chr11:62460912-62461381	ECC-1	luminal epithelium:	n/a	n/a
7	TEAD4	chr11:62461077-62461381	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:62459638..62461949-chr11:62475731..62477777,2	K562	blood:
2	chr11:62459728..62461622-chr11:62472596..62474528,2	MCF-7	breast:
3	chr11:62459147..62462324-chr11:62608122..62609946,3	K562	blood:
4	chr11:62461222..62463498-chr11:62475273..62476885,2	MCF-7	breast:
5	chr11:62431383..62435243-chr11:62459760..62464044,5	K562	blood:
6	chr11:62460824..62462451-chr11:62608122..62610723,2	K562	blood:
7	chr11:62461098..62463928-chr11:62464466..62466072,3	K562	blood:
8	chr11:62431383..62434998-chr11:62461047..62463850,4	K562	blood:
9	chr11:62358226..62360334-chr11:62459590..62462332,2	MCF-7	breast:
10	chr11:62431117..62436333-chr11:62459722..62465529,11	MCF-7	breast:
11	chr11:62455845..62461275-chr11:62472394..62475433,5	K562	blood:

No data

Variant related genes	Relation type
LRRN4CL	TF binding region
BSCL2	TF binding region
ENSG00000255432	Chromatin interaction
ENSG00000162188	Chromatin interaction
ENSG00000255508	Chromatin interaction
ENSG00000168000	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000162194	Chromatin interaction
ENSG00000214756	Chromatin interaction
ENSG00000206597	Chromatin interaction
ENSG00000149016	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11822922	1.00[EUR][1000 genomes]
rs12273912	1.00[EUR][1000 genomes]
rs1787724	1.00[EUR][1000 genomes]
rs2510538	1.00[EUR][1000 genomes]
rs2584915	0.84[ASW][hapmap];0.89[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];1.00[EUR][1000 genomes]
rs2584917	1.00[EUR][1000 genomes]
rs2730030	1.00[EUR][1000 genomes]
rs2956139	1.00[EUR][1000 genomes]
rs2956999	0.88[AFR][1000 genomes]
rs2958240	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4387351	1.00[TSI][hapmap]
rs481272	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs482331	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs486451	0.84[ASW][hapmap];0.89[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];1.00[EUR][1000 genomes]
rs489275	1.00[EUR][1000 genomes]
rs4963309	0.84[ASW][hapmap];0.89[LWK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];1.00[EUR][1000 genomes]
rs506132	1.00[EUR][1000 genomes]
rs507101	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs514401	1.00[EUR][1000 genomes]
rs518780	1.00[EUR][1000 genomes]
rs519473	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs523328	1.00[EUR][1000 genomes]
rs544573	0.82[YRI][hapmap];1.00[EUR][1000 genomes]
rs560618	1.00[EUR][1000 genomes]
rs561385	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs56226867	1.00[EUR][1000 genomes]
rs56262657	1.00[EUR][1000 genomes]
rs564587	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs572513	0.84[ASW][hapmap];0.89[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs573146	0.82[YRI][hapmap];1.00[EUR][1000 genomes]
rs57338459	1.00[EUR][1000 genomes]
rs577071	1.00[EUR][1000 genomes]
rs57858466	1.00[EUR][1000 genomes]
rs592337	0.83[YRI][hapmap];1.00[EUR][1000 genomes]
rs595108	1.00[EUR][1000 genomes]
rs60568977	1.00[EUR][1000 genomes]
rs60668695	1.00[EUR][1000 genomes]
rs619109	1.00[EUR][1000 genomes]
rs646194	1.00[EUR][1000 genomes]
rs692773	1.00[EUR][1000 genomes]
rs694678	1.00[EUR][1000 genomes]
rs73487834	1.00[EUR][1000 genomes]
rs73487878	1.00[EUR][1000 genomes]
rs73487879	1.00[EUR][1000 genomes]
rs73487880	1.00[EUR][1000 genomes]
rs73490026	1.00[EUR][1000 genomes]
rs73502133	1.00[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	nsv915636	chr11:62016992-62713565	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1441 gene(s)	inside rSNPs	diseases
2	nsv532283	chr11:62201358-62863475	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1433 gene(s)	inside rSNPs	diseases
3	nsv532284	chr11:62220043-62630253	Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1401 gene(s)	inside rSNPs	diseases
4	nsv832182	chr11:62295575-62462848	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
5	nsv497903	chr11:62330308-62608042	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	489 gene(s)	inside rSNPs	diseases
6	nsv555174	chr11:62334096-62496519	Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	243 gene(s)	inside rSNPs	diseases
7	nsv897623	chr11:62438819-62603916	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	215 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Response to anti-retroviral therapy (ddI/d4T) in HIV-1 infection (Grade 3 peripheral neuropathy)	24554482	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs575134	C11orf48	cis	lymphoblastoid	seeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:62447000-62472400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:62453600-62462000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr11:62456000-62461800	Weak transcription	Psoas Muscle	Psoas
4	chr11:62456000-62472800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr11:62456000-62472800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr11:62456000-62472800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr11:62456800-62461400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr11:62456800-62461600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr11:62456800-62462000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr11:62456800-62462400	Strong transcription	Brain Germinal Matrix	brain
11	chr11:62456800-62462600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr11:62457000-62462000	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr11:62457000-62462600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr11:62457000-62464400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:62457000-62472600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr11:62457000-62472800	Weak transcription	Small Intestine	intestine
17	chr11:62457200-62461800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr11:62457400-62462000	Strong transcription	Fetal Thymus	thymus
19	chr11:62457400-62462200	Strong transcription	H9 Cell Line	embryonic stem cell
20	chr11:62457400-62462200	Strong transcription	Fetal Intestine Large	intestine
21	chr11:62457400-62462600	Strong transcription	Brain Anterior Caudate	brain
22	chr11:62457600-62461400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr11:62457600-62461400	Strong transcription	Placenta Amnion	Placenta Amnion
24	chr11:62457600-62461600	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr11:62457600-62462000	Weak transcription	Right Atrium	heart
26	chr11:62457600-62462200	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr11:62457600-62462400	Strong transcription	Brain Angular Gyrus	brain
28	chr11:62457800-62461400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr11:62457800-62461400	Strong transcription	Osteobl	bone
30	chr11:62457800-62461600	Strong transcription	K562	blood
31	chr11:62457800-62462000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr11:62457800-62472200	Weak transcription	Fetal Heart	heart
33	chr11:62458000-62462000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr11:62458000-62462200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr11:62458200-62461600	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr11:62458200-62461800	Strong transcription	Placenta	Placenta
37	chr11:62458200-62461800	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr11:62458200-62462600	Strong transcription	Fetal Intestine Small	intestine
39	chr11:62458400-62461400	Strong transcription	Stomach Smooth Muscle	stomach
40	chr11:62458400-62462000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr11:62458400-62462000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr11:62458400-62462400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr11:62458600-62462000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr11:62458600-62462800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr11:62458800-62462000	Strong transcription	Fetal Muscle Leg	muscle
46	chr11:62458800-62462200	Strong transcription	Fetal Muscle Trunk	muscle
47	chr11:62459000-62462200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr11:62459000-62464800	Strong transcription	Fetal Stomach	stomach
49	chr11:62459200-62462000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr11:62459800-62472600	Weak transcription	HUVEC	blood vessel

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