Variant report

Variant	rs41310931
Chromosome Location	chr1:154439338-154439339
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:154299377..154301851-chr1:154439131..154442124,2	MCF-7	breast:
2	chr1:154317108..154317820-chr1:154438724..154439547,2	MCF-7	breast:
3	chr1:154377367..154378131-chr1:154439226..154439911,3	MCF-7	breast:
4	chr1:154377223..154380396-chr1:154438444..154440442,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160712	Chromatin interaction
ENSG00000143515	Chromatin interaction
ENSG00000228013	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11265614	0.89[EUR][1000 genomes]
rs2229237	0.89[EUR][1000 genomes]
rs35938325	0.89[EUR][1000 genomes]
rs41308415	0.89[EUR][1000 genomes]
rs57342848	0.89[EUR][1000 genomes]
rs58229059	0.89[EUR][1000 genomes]
rs58281895	0.89[EUR][1000 genomes]
rs59502179	0.89[EUR][1000 genomes]
rs73014267	0.89[EUR][1000 genomes]
rs73014271	0.89[EUR][1000 genomes]
rs73014279	0.89[EUR][1000 genomes]
rs73016210	0.89[EUR][1000 genomes]
rs73026642	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
2	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
3	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154418000-154440000	Weak transcription	Small Intestine	intestine
2	chr1:154426600-154440600	Weak transcription	Brain Angular Gyrus	brain
3	chr1:154426800-154441200	Weak transcription	Brain Substantia Nigra	brain
4	chr1:154426800-154442200	Weak transcription	HepG2	liver
5	chr1:154426800-154450000	Weak transcription	Fetal Intestine Small	intestine
6	chr1:154427800-154464800	Weak transcription	Ovary	ovary
7	chr1:154429800-154446200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:154431600-154441400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr1:154432000-154442000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr1:154434800-154439600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr1:154435200-154441000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:154435600-154440000	Enhancers	Primary hematopoietic stem cells	blood
13	chr1:154435600-154441400	Enhancers	Fetal Thymus	thymus
14	chr1:154436200-154440800	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr1:154436200-154441000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:154436200-154441200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:154436400-154441800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:154436400-154446400	Weak transcription	NHEK	skin
19	chr1:154436400-154446600	Weak transcription	HMEC	breast
20	chr1:154436600-154439400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr1:154436600-154440600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr1:154436600-154441000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr1:154436600-154441200	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr1:154436600-154441200	Weak transcription	Fetal Brain Male	brain
25	chr1:154436600-154441600	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr1:154436600-154441600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr1:154436600-154446800	Weak transcription	NHDF-Ad	bronchial
28	chr1:154436600-154450600	Weak transcription	HUVEC	blood vessel
29	chr1:154437200-154439400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr1:154437200-154441600	Strong transcription	Lung	lung
31	chr1:154437400-154442000	Weak transcription	Colonic Mucosa	Colon
32	chr1:154437600-154439600	Genic enhancers	Primary monocytes fromperipheralblood	blood
33	chr1:154437800-154439400	Genic enhancers	Stomach Smooth Muscle	stomach
34	chr1:154437800-154440200	Genic enhancers	Monocytes-CD14+_RO01746	blood
35	chr1:154437800-154440400	Enhancers	GM12878-XiMat	blood
36	chr1:154437800-154442800	Enhancers	Brain Hippocampus Middle	brain
37	chr1:154438000-154439400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr1:154438000-154439600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr1:154438000-154442600	Weak transcription	Fetal Stomach	stomach
40	chr1:154438200-154441400	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr1:154438200-154442200	Weak transcription	Stomach Mucosa	stomach
42	chr1:154438400-154440000	Genic enhancers	Primary neutrophils fromperipheralblood	blood
43	chr1:154438400-154440000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr1:154438400-154441000	Weak transcription	Right Ventricle	heart
45	chr1:154438400-154441000	Weak transcription	Spleen	Spleen
46	chr1:154438400-154445800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr1:154438400-154446000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr1:154438400-154457800	Weak transcription	Pancreas	Pancrea
49	chr1:154438400-154458400	Weak transcription	Gastric	stomach
50	chr1:154438400-154463400	Weak transcription	Esophagus	oesophagus

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