Variant report

Variant	rs4656993
Chromosome Location	chr1:161176137-161176138
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EBF1	chr1:161176048-161176167	GM12878	blood:	n/a	chr1:161176148-161176161 chr1:161176148-161176159 chr1:161176150-161176159 chr1:161176150-161176159 chr1:161176150-161176160

No.	Distal block	Cell Line	Cell type
1	chr1:161174340..161177261-chr1:161184177..161187109,2	K562	blood:
2	chr1:161145883..161148987-chr1:161172798..161176306,4	K562	blood:
3	chr1:161175566..161178282-chr1:161184177..161186435,3	K562	blood:
4	chr1:161173950..161176366-chr1:161191214..161193773,2	MCF-7	breast:

Variant related genes	Relation type
NDUFS2	TF binding region
ENSG00000158850	Chromatin interaction
ENSG00000158874	Chromatin interaction
ENSG00000158869	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10797094	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11265564	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12024799	1.00[JPT][hapmap]
rs2501876	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2502806	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs3813622	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4073054	0.87[GIH][hapmap]
rs4233367	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4564157	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4589131	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5082	0.80[GIH][hapmap]
rs7512012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]

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	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4656993	TAGLN2	cis	parietal	SCAN
rs4656993	FCRL3	cis	parietal	SCAN
rs4656993	OR10J5	cis	cerebellum	SCAN
rs4656993	NES	cis	cerebellum	SCAN
rs4656993	B4GALT3	cis	cerebellum	SCAN
rs4656993	DCAF8	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161172800-161176200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:161172800-161176200	Weak transcription	Aorta	Aorta
3	chr1:161172800-161186800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:161172800-161193600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:161173000-161176200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:161173000-161176400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:161173000-161176600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
8	chr1:161173000-161179800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:161173200-161177200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
10	chr1:161173400-161176200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:161173400-161176200	Weak transcription	A549	lung
12	chr1:161173400-161176200	Strong transcription	Osteobl	bone
13	chr1:161173400-161177400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
14	chr1:161173400-161177600	Strong transcription	Brain Inferior Temporal Lobe	brain
15	chr1:161173400-161179400	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr1:161173400-161179600	Strong transcription	Fetal Intestine Large	intestine
17	chr1:161173400-161179800	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr1:161173400-161179800	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr1:161173400-161179800	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr1:161173400-161185200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:161173400-161185400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:161173600-161176200	Weak transcription	Gastric	stomach
23	chr1:161173600-161176200	Weak transcription	Psoas Muscle	Psoas
24	chr1:161173600-161176200	Strong transcription	NH-A	brain
25	chr1:161173600-161177200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:161173600-161177200	Strong transcription	Fetal Kidney	kidney
27	chr1:161173600-161177400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr1:161173600-161177400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
29	chr1:161173600-161177600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr1:161173600-161179200	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr1:161173600-161179800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr1:161173600-161184400	Strong transcription	Primary B cells from peripheral blood	blood
33	chr1:161173600-161184600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr1:161173600-161184800	Strong transcription	Fetal Muscle Trunk	muscle
35	chr1:161173600-161185000	Strong transcription	Fetal Muscle Leg	muscle
36	chr1:161173800-161176200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr1:161173800-161176200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr1:161173800-161176200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:161173800-161176200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr1:161173800-161176200	Strong transcription	Brain Anterior Caudate	brain
41	chr1:161173800-161176200	Weak transcription	Esophagus	oesophagus
42	chr1:161173800-161176200	Weak transcription	Left Ventricle	heart
43	chr1:161173800-161176200	Weak transcription	Lung	lung
44	chr1:161173800-161176200	Weak transcription	Ovary	ovary
45	chr1:161173800-161176200	Weak transcription	Rectal Smooth Muscle	rectum
46	chr1:161173800-161176200	Weak transcription	Small Intestine	intestine
47	chr1:161173800-161176200	Weak transcription	Spleen	Spleen
48	chr1:161173800-161176200	Strong transcription	HSMM	muscle
49	chr1:161173800-161176400	Strong transcription	Placenta	Placenta
50	chr1:161173800-161176600	Genic enhancers	Primary T cells from cord blood	blood

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