Variant report

Variant	rs11102471
Chromosome Location	chr1:112939784-112939785
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:112937855..112940278-chr1:113239914..113242532,2	MCF-7	breast:
2	chr1:112936667..112940657-chr1:113004024..113011069,20	MCF-7	breast:
3	chr1:112934847..112940551-chr1:113160058..113165450,12	MCF-7	breast:
4	chr1:112933576..112940137-chr1:113246857..113251993,14	MCF-7	breast:
5	chr1:112939407..112940147-chr12:6579801..6580494,2	Hela-S3	cervix:
6	chr1:112930309..112940640-chr1:113155859..113164847,24	MCF-7	breast:
7	chr1:112935548..112944315-chr1:113002393..113010397,28	MCF-7	breast:
8	chr1:112938761..112941761-chr1:113247568..113249753,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-WNT2B-2	chr1:112938881-112941439	NONHSAT005231

No data

Variant related genes	Relation type
ENSG00000155363	Chromatin interaction
ENSG00000155366	Chromatin interaction
ENSG00000134245	Chromatin interaction
ENSG00000139190	Chromatin interaction
ENSG00000007341	Chromatin interaction
ENSG00000116489	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1018712	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs11102472	0.82[EUR][1000 genomes]
rs1175629	0.81[EUR][1000 genomes]
rs1177812	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs1177813	0.82[EUR][1000 genomes]
rs12138024	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1412931	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs1419041	0.92[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1475710	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs1572048	0.81[EUR][1000 genomes]
rs1759684	0.81[EUR][1000 genomes]
rs1759688	0.81[EUR][1000 genomes]
rs1759689	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs1759692	0.91[CEU][hapmap]
rs1777608	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs1777615	0.81[EUR][1000 genomes]
rs1891705	0.92[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2026499	0.82[EUR][1000 genomes]
rs2026500	0.82[EUR][1000 genomes]
rs2483328	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs2483332	0.82[EUR][1000 genomes]
rs2483333	0.81[EUR][1000 genomes]
rs2483338	0.84[CEU][hapmap]
rs2483346	0.81[EUR][1000 genomes]
rs2483349	0.81[EUR][1000 genomes]
rs2483350	0.81[EUR][1000 genomes]
rs2483351	0.81[EUR][1000 genomes]
rs2483352	0.81[EUR][1000 genomes]
rs2483356	0.81[EUR][1000 genomes]
rs2483357	0.81[EUR][1000 genomes]
rs2483358	0.81[EUR][1000 genomes]
rs2483359	0.81[EUR][1000 genomes]
rs2483360	0.81[EUR][1000 genomes]
rs2483361	0.81[EUR][1000 genomes]
rs2483362	0.81[EUR][1000 genomes]
rs2488757	0.82[EUR][1000 genomes]
rs2488758	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs2488759	0.83[EUR][1000 genomes]
rs2488761	0.83[EUR][1000 genomes]
rs2488762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2488763	0.84[ASN][1000 genomes]
rs2488765	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2488766	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2488768	0.92[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2488769	0.92[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2488770	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2488786	0.82[CEU][hapmap]
rs2488787	0.92[CEU][hapmap]
rs2488791	0.81[EUR][1000 genomes]
rs2488792	0.81[EUR][1000 genomes]
rs2492502	0.92[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2492503	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2492504	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2492506	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs2492507	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs2492509	0.82[EUR][1000 genomes]
rs2492510	0.82[EUR][1000 genomes]
rs2492511	0.81[EUR][1000 genomes]
rs2492512	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs2492513	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs2492514	0.81[EUR][1000 genomes]
rs2492515	0.82[EUR][1000 genomes]
rs2492516	0.81[EUR][1000 genomes]
rs2492517	0.81[EUR][1000 genomes]
rs2492518	0.81[EUR][1000 genomes]
rs2492519	0.81[EUR][1000 genomes]
rs2492521	0.81[EUR][1000 genomes]
rs2492522	0.81[EUR][1000 genomes]
rs2492523	0.81[EUR][1000 genomes]
rs2492524	0.81[EUR][1000 genomes]
rs2492525	0.81[EUR][1000 genomes]
rs2492529	0.81[EUR][1000 genomes]
rs2492534	0.92[CEU][hapmap]
rs2999472	0.92[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2999476	0.82[EUR][1000 genomes]
rs3122287	0.82[EUR][1000 genomes]
rs55835005	0.81[EUR][1000 genomes]
rs6696624	0.83[EUR][1000 genomes]
rs6703430	0.82[EUR][1000 genomes]
rs7536263	0.81[EUR][1000 genomes]
rs7541222	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs962401	0.82[EUR][1000 genomes]

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	esv13370	chr1:112693290-113246263	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS 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	166 gene(s)	inside rSNPs	diseases
3	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
4	nsv831081	chr1:112934920-113122640	Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11102471	CTTNBP2NL	cis	multi-tissue	Pritchard
rs11102471	CTTNBP2NL	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:112936200-112940000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr1:112937000-112940000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr1:112938000-112940000	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr1:112938000-112940000	Active TSS	H9 Cell Line	embryonic stem cell
5	chr1:112938000-112940000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
6	chr1:112938000-112941000	Active TSS	Aorta	Aorta
7	chr1:112938200-112939800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:112938200-112939800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:112938200-112939800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr1:112938200-112939800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr1:112938200-112939800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:112938200-112939800	Active TSS	Ovary	ovary
13	chr1:112938200-112939800	Active TSS	Psoas Muscle	Psoas
14	chr1:112938200-112939800	Active TSS	Spleen	Spleen
15	chr1:112938200-112940000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr1:112938200-112940000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:112938200-112940000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:112938200-112940000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:112938200-112940000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
20	chr1:112938200-112940000	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr1:112938200-112940200	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr1:112938200-112940200	Active TSS	Right Ventricle	heart
23	chr1:112938200-112940400	Active TSS	H1 Cell Line	embryonic stem cell
24	chr1:112938200-112940400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:112938200-112940400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr1:112938200-112941200	Active TSS	Right Atrium	heart
27	chr1:112938200-112941400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:112938400-112939800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:112938400-112939800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr1:112938400-112939800	Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr1:112938400-112939800	Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr1:112938400-112939800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:112938400-112939800	Active TSS	Brain Substantia Nigra	brain
34	chr1:112938400-112939800	Active TSS	Fetal Brain Male	brain
35	chr1:112938400-112939800	Active TSS	Fetal Kidney	kidney
36	chr1:112938400-112939800	Active TSS	Gastric	stomach
37	chr1:112938400-112939800	Active TSS	A549	lung
38	chr1:112938400-112940000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:112938400-112940000	Active TSS	Esophagus	oesophagus
40	chr1:112938400-112940000	Active TSS	Left Ventricle	heart
41	chr1:112938400-112940000	Active TSS	Lung	lung
42	chr1:112938400-112940000	Active TSS	Pancreas	Pancrea
43	chr1:112938400-112940000	Active TSS	Sigmoid Colon	Sigmoid Colon
44	chr1:112938400-112940000	Active TSS	Small Intestine	intestine
45	chr1:112938400-112940000	Active TSS	Stomach Mucosa	stomach
46	chr1:112938400-112940200	Active TSS	HUES6 Cell Line	embryonic stem cell
47	chr1:112938400-112940200	Active TSS	NHDF-Ad	bronchial
48	chr1:112938400-112940400	Active TSS	HUES64 Cell Line	embryonic stem cell
49	chr1:112938400-112940600	Active TSS	GM12878-XiMat	blood
50	chr1:112938400-112940800	Active TSS	Fetal Intestine Small	intestine

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