Variant report

Variant	rs2041066
Chromosome Location	chr7:112123565-112123566
allele	A/G
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:9)
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	GATA3	chr7:112123379-112123578	SH-SY5Y	brain:	n/a	n/a
2	GATA3	chr7:112123417-112123784	T-47D	breast:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:112089471..112094125-chr7:112120459..112123941,5	MCF-7	breast:
2	chr7:112088410..112092033-chr7:112123451..112127009,4	MCF-7	breast:
3	chr7:112121071..112126030-chr7:112126598..112131851,6	K562	blood:
4	chr7:112088943..112098465-chr7:112111106..112127214,31	K562	blood:
5	chr7:112120506..112122377-chr7:112122627..112125430,3	K562	blood:
6	chr7:112121639..112123962-chr7:112132170..112134503,2	K562	blood:
7	chr7:112122239..112125298-chr7:112125883..112129241,4	MCF-7	breast:
8	chr7:112114860..112117053-chr7:112123342..112124969,2	K562	blood:
9	chr7:112122370..112125277-chr7:112129500..112134032,5	K562	blood:

No data

Variant related genes	Relation type
LSMEM1	TF binding region
ENSG00000006652	Chromatin interaction
ENSG00000181016	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1005659	0.84[MEX][hapmap];0.84[AMR][1000 genomes]
rs1005661	0.84[MEX][hapmap];0.84[AMR][1000 genomes]
rs1024569	0.82[AMR][1000 genomes]
rs1024570	0.82[AMR][1000 genomes]
rs1024571	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1024572	0.82[AMR][1000 genomes]
rs1029631	0.84[AMR][1000 genomes]
rs10487291	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1054043	0.85[AMR][1000 genomes]
rs10953712	0.84[AMR][1000 genomes]
rs10953713	0.81[AMR][1000 genomes]
rs11514940	0.84[AMR][1000 genomes]
rs11773335	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12154294	0.83[AMR][1000 genomes]
rs12531160	1.00[ASN][1000 genomes]
rs12532656	1.00[ASN][1000 genomes]
rs12539263	0.81[CEU][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs16873394	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17132179	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1963308	0.81[AMR][1000 genomes]
rs2041067	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2190587	0.85[AMR][1000 genomes]
rs3128384	0.98[LWK][hapmap];0.96[MKK][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes]
rs36095669	0.84[AMR][1000 genomes]
rs3807206	0.84[AMR][1000 genomes]
rs4727774	0.85[AMR][1000 genomes]
rs6944364	0.84[MEX][hapmap]
rs6956741	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6973615	0.83[AMR][1000 genomes]
rs6978173	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs73201473	1.00[ASN][1000 genomes]
rs73201481	1.00[ASN][1000 genomes]
rs7455170	0.84[AMR][1000 genomes]
rs7817	0.84[MEX][hapmap];0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531436	chr7:111856171-112585407	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	105 gene(s)	inside rSNPs	diseases
2	nsv1030033	chr7:112092709-112140430	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2041066	C7orf53	cis	cerebellum	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:112100600-112135000	Weak transcription	Esophagus	oesophagus
2	chr7:112110600-112124600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:112111200-112127200	Weak transcription	Fetal Brain Male	brain
4	chr7:112112600-112129000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr7:112113200-112124600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr7:112113200-112124800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr7:112113200-112125000	Weak transcription	Right Ventricle	heart
8	chr7:112113400-112127600	Weak transcription	Spleen	Spleen
9	chr7:112114400-112132000	Weak transcription	HepG2	liver
10	chr7:112114600-112125000	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr7:112116800-112132200	Weak transcription	Fetal Intestine Small	intestine
12	chr7:112117200-112125200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr7:112117200-112127200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr7:112117200-112128800	Weak transcription	Dnd41	blood
15	chr7:112117400-112124600	Weak transcription	Primary T cells from cord blood	blood
16	chr7:112117400-112124600	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr7:112117400-112124800	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr7:112117400-112130800	Weak transcription	Thymus	Thymus
19	chr7:112117600-112124800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr7:112117600-112125000	Weak transcription	Lung	lung
21	chr7:112117600-112125800	Weak transcription	Fetal Stomach	stomach
22	chr7:112117600-112131600	Weak transcription	Fetal Intestine Large	intestine
23	chr7:112118000-112125000	Weak transcription	Placenta	Placenta
24	chr7:112118200-112124000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr7:112118200-112125000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr7:112118800-112141600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr7:112119800-112124800	Weak transcription	Fetal Thymus	thymus
28	chr7:112120600-112123600	Enhancers	Muscle Satellite Cultured Cells	--
29	chr7:112120600-112126200	Enhancers	NHDF-Ad	bronchial
30	chr7:112120800-112124800	Enhancers	Hela-S3	cervix
31	chr7:112120800-112126000	Weak transcription	Primary B cells from cord blood	blood
32	chr7:112121000-112123600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr7:112121000-112124800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr7:112121000-112124800	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr7:112121000-112124800	Weak transcription	Left Ventricle	heart
36	chr7:112121000-112124800	Weak transcription	Pancreas	Pancrea
37	chr7:112121000-112126000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr7:112121000-112126000	Enhancers	Fetal Heart	heart
39	chr7:112121000-112136200	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr7:112121200-112125000	Enhancers	HSMM	muscle
41	chr7:112121200-112132000	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr7:112121400-112125200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr7:112121600-112129600	Weak transcription	Liver	Liver
44	chr7:112121800-112123600	Weak transcription	Aorta	Aorta
45	chr7:112122200-112123600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr7:112122200-112124800	Weak transcription	Brain Angular Gyrus	brain
47	chr7:112122200-112124800	Weak transcription	Small Intestine	intestine
48	chr7:112122400-112123600	Weak transcription	Psoas Muscle	Psoas
49	chr7:112122400-112124600	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr7:112122400-112124600	Weak transcription	Brain Substantia Nigra	brain

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