Variant report

Variant	rs3806161
Chromosome Location	chr1:75200785-75200786
allele	A/C
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	POLR2A	chr1:75200355-75200800	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr1:75196850-75200950	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:75196987-75201662	GM12891	blood:	n/a	n/a
4	WRNIP1	chr1:75200249-75200801	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:75182455..75184516-chr1:75199218..75200932,2	K562	blood:
2	chr1:75197578..75200968-chr1:75201632..75206969,6	MCF-7	breast:
3	chr1:74977554..74979985-chr1:75198825..75201036,2	K562	blood:
4	chr1:75200664..75203474-chr1:76250808..76253106,2	K562	blood:

Variant related genes	Relation type
TYW3	TF binding region
CRYZ	TF binding region
ENSG00000162623	Chromatin interaction
ENSG00000162621	Chromatin interaction
ENSG00000206620	Chromatin interaction
ENSG00000137955	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11162945	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1122338	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1133891	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11485264	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11485299	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12034724	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12043726	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13375787	0.82[AMR][1000 genomes]
rs1359750	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1581870	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2032969	0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs28374065	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28436025	0.82[AMR][1000 genomes]
rs28445096	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28515016	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28563168	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28575168	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28719150	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28740807	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28804147	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28810187	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3819946	0.84[AMR][1000 genomes]
rs3819947	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4650004	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4650007	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4650287	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4650288	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58715708	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60292279	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6681874	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67696801	0.82[AMR][1000 genomes]
rs745108	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7535692	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7540514	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs768223	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9647	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][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	nsv1011745	chr1:74730942-75477618	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv535003	chr1:74730942-75477618	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv830259	chr1:75089177-75241062	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv1851105	chr1:75152186-75302921	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3806161	TYW3	cis	Heart Left Ventricle	GTEx
rs3806161	TYW3	cis	Artery Tibial	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75197800-75200800	Active TSS	NHLF	lung
2	chr1:75197800-75201800	Active TSS	GM12878-XiMat	blood
3	chr1:75199200-75203000	Weak transcription	Spleen	Spleen
4	chr1:75199400-75203000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:75199400-75203000	Weak transcription	Lung	lung
6	chr1:75199400-75203400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:75199400-75203800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:75199600-75200800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:75199600-75200800	Flanking Active TSS	Hela-S3	cervix
10	chr1:75199600-75203000	Weak transcription	Left Ventricle	heart
11	chr1:75199600-75203000	Weak transcription	Pancreas	Pancrea
12	chr1:75199600-75203200	Weak transcription	Esophagus	oesophagus
13	chr1:75199600-75203200	Weak transcription	Gastric	stomach
14	chr1:75199600-75206000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:75199800-75207800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:75200000-75200800	Enhancers	Primary T cells fromperipheralblood	blood
17	chr1:75200000-75200800	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr1:75200000-75200800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:75200000-75200800	Enhancers	Adipose Nuclei	Adipose
20	chr1:75200000-75200800	Enhancers	Fetal Muscle Leg	muscle
21	chr1:75200000-75201000	Enhancers	Duodenum Mucosa	Duodenum
22	chr1:75200000-75201400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr1:75200000-75201400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr1:75200000-75202400	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr1:75200000-75202800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:75200000-75202800	Weak transcription	Fetal Muscle Trunk	muscle
27	chr1:75200000-75202800	Weak transcription	Placenta	Placenta
28	chr1:75200000-75203000	Weak transcription	Thymus	Thymus
29	chr1:75200000-75203200	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr1:75200000-75231600	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr1:75200200-75200800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:75200200-75200800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr1:75200200-75200800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr1:75200200-75200800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr1:75200200-75200800	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr1:75200200-75200800	Enhancers	Colon Smooth Muscle	Colon
37	chr1:75200200-75200800	Enhancers	Fetal Brain Female	brain
38	chr1:75200200-75200800	Enhancers	Ovary	ovary
39	chr1:75200200-75200800	Enhancers	Psoas Muscle	Psoas
40	chr1:75200200-75200800	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr1:75200200-75200800	Enhancers	HSMM	muscle
42	chr1:75200200-75201000	Enhancers	Brain Hippocampus Middle	brain
43	chr1:75200200-75201000	Active TSS	Brain Inferior Temporal Lobe	brain
44	chr1:75200200-75201600	Enhancers	Primary T cells from cord blood	blood
45	chr1:75200200-75201600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr1:75200200-75201600	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr1:75200200-75201600	Enhancers	Brain Cingulate Gyrus	brain
48	chr1:75200200-75201800	Enhancers	Liver	Liver
49	chr1:75200200-75201800	Enhancers	HepG2	liver
50	chr1:75200200-75202400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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