Variant report

Variant	rs241715
Chromosome Location	chr22:33383563-33383564
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:33382445..33385028-chr22:33386160..33388841,3	MCF-7	breast:
2	chr22:33379303..33380936-chr22:33382275..33384664,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs133924	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs133925	0.81[ASN][1000 genomes]
rs133926	0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs133927	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs133929	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs133931	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs133934	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs133936	0.89[ASN][1000 genomes]
rs133937	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.89[ASN][1000 genomes]
rs133938	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs133941	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs133966	0.81[CEU][hapmap];0.84[CHB][hapmap]
rs1365837	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs137552	0.84[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs241707	0.85[ASW][hapmap];0.88[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs241708	0.87[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs241709	0.88[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.80[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs241711	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs241712	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[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]
rs241714	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[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]
rs241717	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs241721	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs241722	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs241725	0.86[CHB][hapmap]
rs241727	0.86[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs241729	0.86[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs241731	0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs241732	0.86[ASW][hapmap];0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs241756	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs241758	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs241759	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs241760	0.88[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs241764	0.86[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs241766	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs241767	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4518061	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs470004	0.92[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs5754366	0.85[ASN][1000 genomes]
rs5754377	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs5998684	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs739143	0.85[CEU][hapmap];0.84[CHB][hapmap]
rs9609676	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][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	nsv531568	chr22:33336868-33480272	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv531587	chr22:33346710-33809338	Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs241715	THOC5	cis	parietal	SCAN
rs241715	NF2	cis	cerebellum	SCAN
rs241715	SLC5A1	cis	parietal	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:33354600-33387400	Weak transcription	Fetal Brain Female	brain
2	chr22:33380400-33383600	Enhancers	Placenta Amnion	Placenta Amnion
3	chr22:33380400-33384000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr22:33380800-33389200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr22:33381000-33383600	Enhancers	Fetal Lung	lung
6	chr22:33381000-33383800	Enhancers	Fetal Stomach	stomach
7	chr22:33381000-33385400	Enhancers	NHEK	skin
8	chr22:33381200-33383800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr22:33381400-33385200	Enhancers	Fetal Muscle Leg	muscle
10	chr22:33381400-33385400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr22:33381600-33383600	Enhancers	Fetal Intestine Small	intestine
12	chr22:33381600-33383600	Enhancers	Fetal Muscle Trunk	muscle
13	chr22:33381600-33383800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr22:33381600-33384000	Enhancers	Placenta	Placenta
15	chr22:33381800-33383600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr22:33381800-33383600	Enhancers	Brain Hippocampus Middle	brain
17	chr22:33381800-33383600	Enhancers	Fetal Brain Male	brain
18	chr22:33381800-33383600	Enhancers	Hela-S3	cervix
19	chr22:33381800-33383800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr22:33381800-33383800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr22:33381800-33383800	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr22:33381800-33383800	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr22:33381800-33383800	Enhancers	Brain Germinal Matrix	brain
24	chr22:33381800-33383800	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr22:33381800-33384000	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr22:33381800-33385000	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr22:33381800-33386600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr22:33381800-33389200	Enhancers	HMEC	breast
29	chr22:33382000-33383600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr22:33382000-33383600	Enhancers	HSMM	muscle
31	chr22:33382000-33383800	Enhancers	H1 Cell Line	embryonic stem cell
32	chr22:33382000-33383800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr22:33382000-33383800	Enhancers	HSMMtube	muscle
34	chr22:33382000-33384000	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr22:33382000-33390200	Weak transcription	Right Atrium	heart
36	chr22:33382200-33383600	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr22:33382200-33383800	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr22:33382200-33384000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr22:33382200-33384000	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr22:33382400-33383600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr22:33382400-33383600	Enhancers	Brain Anterior Caudate	brain
42	chr22:33382400-33383800	Enhancers	H9 Cell Line	embryonic stem cell
43	chr22:33382400-33383800	Enhancers	Brain Cingulate Gyrus	brain
44	chr22:33382400-33384000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr22:33382400-33384800	Weak transcription	Esophagus	oesophagus
46	chr22:33382400-33387600	Weak transcription	NHDF-Ad	bronchial
47	chr22:33382400-33392400	Weak transcription	Lung	lung
48	chr22:33382400-33404200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr22:33382600-33383600	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr22:33382600-33384600	Weak transcription	Spleen	Spleen

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