Variant report

Variant	rs768223
Chromosome Location	chr1:75194035-75194036
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:75192924..75196422-chr1:75198121..75200705,3	MCF-7	breast:
2	chr1:75169904..75171834-chr1:75191758..75194711,2	K562	blood:

Variant related genes	Relation type
ENSG00000162623	Chromatin interaction
ENSG00000116791	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11162945	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1122338	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1133891	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11485264	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11485299	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12034724	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12043726	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[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];0.89[ASN][1000 genomes]
rs1581870	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2032969	0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs28374065	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28436025	0.82[AMR][1000 genomes]
rs28445096	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28515016	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28563168	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28575168	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28719150	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28740807	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28804147	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28810187	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3806161	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3819946	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3819947	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4650004	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4650007	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4650287	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4650288	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58715708	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60292279	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6681874	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67696801	0.82[AMR][1000 genomes]
rs745108	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7535692	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7540514	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9647	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv871152	chr1:75152186-75197533	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
5	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
rs768223	TYW3	cis	Heart Left Ventricle	GTEx
rs768223	TYW3	cis	Artery Tibial	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75166600-75194800	Weak transcription	Esophagus	oesophagus
2	chr1:75167000-75197200	Weak transcription	Right Ventricle	heart
3	chr1:75171000-75197200	Weak transcription	Brain Angular Gyrus	brain
4	chr1:75174800-75198000	Weak transcription	Thymus	Thymus
5	chr1:75175400-75196000	Weak transcription	HSMMtube	muscle
6	chr1:75180000-75196000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr1:75180400-75197200	Weak transcription	Psoas Muscle	Psoas
8	chr1:75183000-75198400	Weak transcription	Fetal Brain Male	brain
9	chr1:75187200-75195400	Weak transcription	HMEC	breast
10	chr1:75187400-75197200	Weak transcription	Stomach Mucosa	stomach
11	chr1:75187800-75197200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr1:75188000-75194400	Weak transcription	Small Intestine	intestine
13	chr1:75188200-75195800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:75188200-75196000	Weak transcription	HSMM	muscle
15	chr1:75188200-75197200	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr1:75188200-75198000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr1:75188400-75195400	Weak transcription	K562	blood
18	chr1:75188400-75196800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr1:75188400-75197200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr1:75188400-75198000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:75188800-75195000	ZNF genes & repeats	GM12878-XiMat	blood
22	chr1:75189000-75197200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr1:75189200-75196400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr1:75189400-75194400	Weak transcription	NHLF	lung
25	chr1:75189400-75194600	Weak transcription	Brain Substantia Nigra	brain
26	chr1:75189400-75194800	Weak transcription	Osteobl	bone
27	chr1:75189400-75195000	Weak transcription	Rectal Smooth Muscle	rectum
28	chr1:75189400-75195400	Weak transcription	NHEK	skin
29	chr1:75189400-75195800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr1:75189400-75197200	Weak transcription	Left Ventricle	heart
31	chr1:75189400-75197400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr1:75189600-75194200	Weak transcription	Stomach Smooth Muscle	stomach
33	chr1:75189600-75194600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr1:75189600-75195800	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr1:75189600-75195800	Weak transcription	Colon Smooth Muscle	Colon
36	chr1:75189600-75195800	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr1:75189600-75197200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr1:75189600-75197400	Weak transcription	Brain Hippocampus Middle	brain
39	chr1:75189800-75195400	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr1:75189800-75195600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr1:75189800-75196800	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr1:75190000-75195800	Weak transcription	Fetal Kidney	kidney
43	chr1:75190600-75194200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr1:75190600-75194600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:75190800-75194200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:75190800-75195600	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr1:75190800-75196000	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr1:75191000-75194200	Weak transcription	A549	lung
49	chr1:75191000-75194200	Weak transcription	NHDF-Ad	bronchial
50	chr1:75191200-75195600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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