Variant report

Variant	rs4972477
Chromosome Location	chr2:173159345-173159346
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:173156581..173161480-chr2:173162847..173166156,5	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10930540	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10930541	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10930542	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10930545	0.86[EUR][1000 genomes]
rs11674489	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11674629	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11674681	0.83[CEU][hapmap];1.00[CHB][hapmap];0.80[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11677934	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11677943	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11685584	0.84[CEU][hapmap];0.92[GIH][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12624040	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13384490	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4427989	0.83[CHD][hapmap]
rs4429441	0.91[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4438453	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4447582	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4450575	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4538169	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4594405	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4619572	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4972774	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4972775	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56239652	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57101510	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7425702	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4972477	CHRNA1	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173151400-173168000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:173153600-173160800	Weak transcription	Right Atrium	heart
3	chr2:173158000-173160800	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr2:173158200-173160800	Enhancers	Pancreas	Pancrea
5	chr2:173158400-173159400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:173158400-173159400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:173158400-173159400	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr2:173158400-173159400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr2:173158400-173159400	Enhancers	Fetal Intestine Large	intestine
10	chr2:173158400-173159400	Enhancers	Fetal Lung	lung
11	chr2:173158400-173159400	Enhancers	Fetal Stomach	stomach
12	chr2:173158400-173159400	Enhancers	HMEC	breast
13	chr2:173158400-173159400	Enhancers	Monocytes-CD14+_RO01746	blood
14	chr2:173158400-173159800	Enhancers	Fetal Intestine Small	intestine
15	chr2:173158600-173159400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr2:173158600-173159400	Enhancers	Duodenum Mucosa	Duodenum
17	chr2:173158600-173159400	Enhancers	Placenta	Placenta
18	chr2:173158600-173159400	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr2:173158600-173159400	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr2:173158600-173159400	Enhancers	Osteobl	bone
21	chr2:173158600-173161000	Enhancers	Stomach Mucosa	stomach
22	chr2:173158800-173159800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr2:173159200-173159400	Bivalent Enhancer	Brain Hippocampus Middle	brain
24	chr2:173159200-173160600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr2:173159200-173160600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr2:173159200-173160600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr2:173159200-173160600	Weak transcription	NHEK	skin
28	chr2:173159200-173160800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr2:173159200-173162200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr2:173159200-173162200	Weak transcription	Ovary	ovary
31	chr2:173159200-173164400	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr2:173159200-173164600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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