Variant report

Variant	rs875883
Chromosome Location	chr1:247460356-247460357
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	chr1:247459842..247461547-chr1:247511493..247513856,2	K562	blood:
2	chr1:247459823..247461547-chr1:247511493..247514413,3	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 11 )

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

rs_ID	r²[population]
rs10754542	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10754544	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs10924983	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10924985	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10924989	0.86[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs11578583	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1192830	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1192831	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1192832	0.82[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12035515	0.86[ASN][1000 genomes]
rs1204493	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1341173	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1616299	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1771929	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1771943	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1771948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1778544	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1778546	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1778549	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2153631	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2799540	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3850824	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4320815	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4925532	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4925533	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4925534	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4925615	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4925621	0.83[ASN][1000 genomes]
rs56037169	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56399534	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6674425	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6692645	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74163745	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7418221	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7528202	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7540329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7552292	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9426180	1.00[CEU][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9426181	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9426182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9426233	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9725334	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[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	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv833126	chr1:247273084-247476150	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	n/a
3	esv3411043	chr1:247382851-247517729	Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a
4	esv3378684	chr1:247382994-247518438	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a
5	nsv833137	chr1:247437317-247607428	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	n/a

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs875883	ZNF496	cis	Esophagus Muscularis	GTEx
rs875883	MAP1LC3C	cis	parietal	SCAN
rs875883	ZNF496	cis	Thyroid	GTEx
rs875883	ZNF496	cis	lung	GTEx
rs875883	ZNF496	cis	Skin Sun Exposed Lower leg	GTEx
rs875883	EDIL3	trans	lymphoblastoid	RTeQTL
rs875883	EFCAB2	cis	parietal	SCAN
rs875883	ZNF496	cis	cerebellum	SCAN
rs875883	OR2T11	cis	parietal	SCAN
rs875883	ZNF496	cis	parietal	SCAN
rs875883	ZNF496	cis	Nerve Tibial	GTEx

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247449200-247462000	Weak transcription	Primary T cells from cord blood	blood
2	chr1:247449400-247460800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr1:247449600-247462400	Weak transcription	Brain Angular Gyrus	brain
4	chr1:247451000-247460800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:247451600-247460400	Weak transcription	Fetal Muscle Leg	muscle
6	chr1:247452400-247460800	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr1:247452600-247460800	Weak transcription	Brain Germinal Matrix	brain
8	chr1:247452600-247461200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:247452800-247462000	Weak transcription	Brain Hippocampus Middle	brain
10	chr1:247453000-247460800	Weak transcription	Fetal Brain Female	brain
11	chr1:247453000-247462000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr1:247453200-247460400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:247453400-247462000	Weak transcription	Colon Smooth Muscle	Colon
14	chr1:247453400-247463000	Weak transcription	Brain Substantia Nigra	brain
15	chr1:247454200-247462600	Weak transcription	Pancreas	Pancrea
16	chr1:247454400-247461800	Enhancers	Fetal Thymus	thymus
17	chr1:247455000-247470400	Weak transcription	Fetal Brain Male	brain
18	chr1:247455200-247461000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr1:247455200-247463000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
20	chr1:247455400-247461200	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr1:247455600-247462600	Enhancers	H9 Cell Line	embryonic stem cell
22	chr1:247455800-247460800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr1:247455800-247462200	Enhancers	H1 Cell Line	embryonic stem cell
24	chr1:247455800-247462600	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr1:247455800-247464200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr1:247456000-247462000	Weak transcription	Lung	lung
27	chr1:247456000-247493400	Weak transcription	Right Atrium	heart
28	chr1:247456200-247460800	Weak transcription	Fetal Muscle Trunk	muscle
29	chr1:247456200-247462200	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr1:247456600-247471400	Weak transcription	Fetal Heart	heart
31	chr1:247456800-247462000	Weak transcription	Ovary	ovary
32	chr1:247456800-247462200	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr1:247456800-247462400	Weak transcription	Duodenum Mucosa	Duodenum
34	chr1:247457000-247460400	Weak transcription	Fetal Stomach	stomach
35	chr1:247457000-247465000	Weak transcription	Hela-S3	cervix
36	chr1:247457800-247463200	Weak transcription	Placenta	Placenta
37	chr1:247457800-247466000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:247458000-247461600	Weak transcription	Aorta	Aorta
39	chr1:247458000-247466800	Weak transcription	HSMMtube	muscle
40	chr1:247458200-247462000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr1:247458200-247462200	Weak transcription	HSMM	muscle
42	chr1:247458200-247462400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:247458200-247463000	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr1:247458600-247461000	Weak transcription	Right Ventricle	heart
45	chr1:247458800-247462000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr1:247459000-247460600	Weak transcription	A549	lung
47	chr1:247459000-247460800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr1:247459000-247461000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:247459000-247461600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr1:247459000-247462200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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