Variant report

Variant	rs3014576
Chromosome Location	chr1:241679889-241679890
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:241616113..241618649-chr1:241678883..241680666,2	K562	blood:
2	chr1:241677220..241680834-chr1:241684726..241688550,4	K562	blood:
3	chr1:241654504..241656882-chr1:241679445..241682289,2	K562	blood:
4	chr1:241678718..241680701-chr1:241800665..241802574,2	K562	blood:
5	chr1:241657615..241659200-chr1:241678785..241681032,2	K562	blood:

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10157091	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10926494	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2144	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2341935	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2994981	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2994984	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2994986	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2994990	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3014577	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv918034	chr1:241072791-242005532	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
2	nsv997966	chr1:241100739-242087629	Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	nsv949442	chr1:241432051-241730054	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1002214	chr1:241458939-242099790	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv549460	chr1:241494578-241833287	Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv1009579	chr1:241499537-241824631	Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv530112	chr1:241522031-241840269	Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv873368	chr1:241533392-242195928	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
9	nsv873371	chr1:241667244-241747838	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3014576	RP11-527D7.1	cis	Nerve Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:241657000-241680000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr1:241657400-241680000	Strong transcription	Primary B cells from cord blood	blood
3	chr1:241659000-241682000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:241661200-241681400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr1:241664800-241680600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:241667400-241680800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:241667400-241681800	Weak transcription	Fetal Brain Male	brain
8	chr1:241667600-241681800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:241667800-241682000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr1:241668000-241680600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr1:241668000-241682000	Weak transcription	Pancreas	Pancrea
12	chr1:241668000-241682200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:241668000-241682200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:241668000-241682200	Weak transcription	Esophagus	oesophagus
15	chr1:241668800-241680400	Weak transcription	Fetal Stomach	stomach
16	chr1:241671800-241682000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr1:241672000-241681200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:241672000-241681200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr1:241672000-241681200	Weak transcription	Stomach Mucosa	stomach
20	chr1:241672000-241681400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr1:241672000-241682000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr1:241672200-241681800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr1:241672800-241681200	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr1:241673200-241682200	Weak transcription	Spleen	Spleen
25	chr1:241674800-241681400	Weak transcription	Thymus	Thymus
26	chr1:241674800-241681800	Weak transcription	Small Intestine	intestine
27	chr1:241674800-241682000	Weak transcription	Colonic Mucosa	Colon
28	chr1:241675200-241681400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr1:241675400-241681800	Weak transcription	Ovary	ovary
30	chr1:241675600-241681400	Weak transcription	HSMMtube	muscle
31	chr1:241675600-241681800	Weak transcription	Brain Germinal Matrix	brain
32	chr1:241675800-241680600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr1:241675800-241680600	Weak transcription	Colon Smooth Muscle	Colon
34	chr1:241675800-241680600	Weak transcription	Rectal Smooth Muscle	rectum
35	chr1:241675800-241680800	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr1:241675800-241680800	Weak transcription	Fetal Kidney	kidney
37	chr1:241675800-241681200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr1:241675800-241681200	Weak transcription	Brain Hippocampus Middle	brain
39	chr1:241675800-241681400	Weak transcription	Brain Angular Gyrus	brain
40	chr1:241675800-241681800	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr1:241675800-241681800	Weak transcription	Left Ventricle	heart
42	chr1:241675800-241681800	Weak transcription	Stomach Smooth Muscle	stomach
43	chr1:241675800-241682000	Weak transcription	Aorta	Aorta
44	chr1:241675800-241682200	Weak transcription	Lung	lung
45	chr1:241676000-241680600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr1:241676000-241680600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr1:241676000-241680800	Weak transcription	Primary T cells from cord blood	blood
48	chr1:241676000-241681200	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr1:241676000-241681200	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr1:241676000-241681400	Weak transcription	Primary hematopoietic stem cells	blood

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