Variant report

Variant	rs1149618
Chromosome Location	chr11:76500875-76500876
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:76498272-76500991	HepG2	liver:	n/a	n/a
2	RCOR1	chr11:76500563-76500882	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:76464979..76468586-chr11:76498537..76501368,3	MCF-7	breast:
2	chr11:76475834..76477640-chr11:76498585..76500944,2	K562	blood:
3	chr11:76498398..76500983-chr11:76629016..76630524,2	MCF-7	breast:
4	chr11:76500135..76502370-chr11:76510962..76513863,2	MCF-7	breast:
5	chr11:76497872..76501557-chr11:76570027..76573455,3	K562	blood:
6	chr11:76499655..76502011-chr11:76503724..76505940,3	K562	blood:

No data

Variant related genes	Relation type
TSKU	TF binding region
ENSG00000078124	Chromatin interaction
ENSG00000261578	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10899287	0.87[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap]
rs11236933	1.00[YRI][hapmap]
rs1149597	1.00[ASW][hapmap];0.89[CEU][hapmap]
rs1149599	1.00[ASW][hapmap];0.83[CEU][hapmap]
rs1149605	0.89[CEU][hapmap]
rs1149606	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs1149608	0.86[EUR][1000 genomes]
rs1149609	0.92[EUR][1000 genomes]
rs1149610	0.92[EUR][1000 genomes]
rs1149612	0.87[EUR][1000 genomes]
rs1149614	0.96[EUR][1000 genomes]
rs1149615	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs1149616	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1149617	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1149619	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1149622	0.87[CHB][hapmap];0.91[CHD][hapmap];0.83[JPT][hapmap]
rs1224955	1.00[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs12577786	1.00[ASW][hapmap]
rs1664081	0.91[GIH][hapmap]
rs1687692	0.87[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs1687693	0.85[ASN][1000 genomes]
rs34909318	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35044108	0.83[ASN][1000 genomes]
rs3740776	0.83[EUR][1000 genomes]
rs3740777	0.92[EUR][1000 genomes]
rs733454	1.00[ASW][hapmap]
rs7925095	1.00[YRI][hapmap]
rs7925436	1.00[YRI][hapmap]
rs881930	0.89[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897931	chr11:76489673-76540708	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1149618	LRRC54	cis	multi-tissue	Pritchard
rs1149618	RP11-21L23.3	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:76495400-76501800	Transcr. at gene 5' and 3'	A549	lung
2	chr11:76496000-76501000	Enhancers	Right Ventricle	heart
3	chr11:76496000-76506800	Weak transcription	Aorta	Aorta
4	chr11:76496200-76503600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr11:76496200-76513800	Weak transcription	Fetal Kidney	kidney
6	chr11:76496400-76501000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr11:76496400-76501800	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr11:76496400-76504000	Weak transcription	HSMMtube	muscle
9	chr11:76496600-76504400	Weak transcription	HUVEC	blood vessel
10	chr11:76496600-76509800	Weak transcription	Colon Smooth Muscle	Colon
11	chr11:76496800-76501200	Enhancers	Duodenum Mucosa	Duodenum
12	chr11:76496800-76501400	Enhancers	Colonic Mucosa	Colon
13	chr11:76496800-76504200	Weak transcription	HSMM	muscle
14	chr11:76496800-76507400	Enhancers	Stomach Mucosa	stomach
15	chr11:76496800-76510000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr11:76497400-76501200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr11:76497400-76502200	Weak transcription	Brain Germinal Matrix	brain
18	chr11:76498000-76503200	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr11:76498000-76504000	Weak transcription	Stomach Smooth Muscle	stomach
20	chr11:76498200-76501600	Genic enhancers	K562	blood
21	chr11:76498200-76501800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr11:76498200-76502600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr11:76498400-76505800	Enhancers	Placenta	Placenta
24	chr11:76498600-76501000	Enhancers	Fetal Intestine Large	intestine
25	chr11:76499000-76501000	Weak transcription	Hela-S3	cervix
26	chr11:76499000-76501600	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr11:76499000-76510200	Weak transcription	Thymus	Thymus
28	chr11:76499200-76501200	Enhancers	Liver	Liver
29	chr11:76499400-76501400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr11:76499400-76502600	Weak transcription	Osteobl	bone
31	chr11:76499400-76502800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr11:76499400-76504200	Enhancers	Esophagus	oesophagus
33	chr11:76499600-76501800	Enhancers	Small Intestine	intestine
34	chr11:76499600-76502800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr11:76499800-76501400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr11:76499800-76502200	Enhancers	HMEC	breast
37	chr11:76499800-76502600	Weak transcription	NH-A	brain
38	chr11:76499800-76503200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr11:76499800-76503800	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr11:76499800-76504200	Weak transcription	Fetal Brain Male	brain
41	chr11:76500000-76501000	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr11:76500000-76501200	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr11:76500000-76501200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr11:76500000-76501400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr11:76500000-76501400	Weak transcription	Spleen	Spleen
46	chr11:76500000-76502600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr11:76500000-76503000	Weak transcription	NHDF-Ad	bronchial
48	chr11:76500000-76504600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr11:76500000-76506400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr11:76500200-76501200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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