Variant report

Variant	rs2223908
Chromosome Location	chr1:94270165-94270166
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	chr1:94145037..94147485-chr1:94269296..94271164,2	MCF-7	breast:
2	chr1:94269224..94270816-chr1:94271541..94273859,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137936	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10874795	0.91[ASN][1000 genomes]
rs1108527	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1108528	0.84[EUR][1000 genomes]
rs11164994	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11165001	0.97[ASN][1000 genomes]
rs11165019	0.91[ASN][1000 genomes]
rs12079584	0.91[ASN][1000 genomes]
rs12239830	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1467129	0.86[AMR][1000 genomes]
rs17100397	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17110408	0.97[ASN][1000 genomes]
rs17304770	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17878271	0.87[EUR][1000 genomes]
rs17878294	0.87[EUR][1000 genomes]
rs17881810	0.87[EUR][1000 genomes]
rs17884788	0.87[EUR][1000 genomes]
rs17885151	0.87[EUR][1000 genomes]
rs17886352	0.87[EUR][1000 genomes]
rs1877605	0.86[EUR][1000 genomes]
rs3761913	0.90[EUR][1000 genomes]
rs41292665	0.92[EUR][1000 genomes]
rs57870303	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61425457	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61781046	0.83[AMR][1000 genomes]
rs61781048	0.83[EUR][1000 genomes]
rs61781049	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61781051	0.98[EUR][1000 genomes]
rs61781053	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61781054	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61781055	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61781056	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61781057	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61782162	0.92[EUR][1000 genomes]
rs61782163	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs61782164	0.90[EUR][1000 genomes]
rs61782165	0.87[EUR][1000 genomes]
rs61782398	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61782399	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61782400	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61782403	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61782404	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61782405	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61782410	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61782413	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61782449	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61782450	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61782451	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61782458	0.90[EUR][1000 genomes]
rs61782459	0.89[EUR][1000 genomes]
rs6660794	0.97[ASN][1000 genomes]
rs6671839	0.97[ASN][1000 genomes]
rs6674149	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6689215	0.94[ASN][1000 genomes]
rs6689746	0.97[ASN][1000 genomes]
rs6703468	0.97[ASN][1000 genomes]
rs717913	0.97[ASN][1000 genomes]
rs72723114	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72723118	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72723125	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72723138	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72723157	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72723165	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72723169	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72723178	0.92[EUR][1000 genomes]
rs72967397	0.91[ASN][1000 genomes]
rs7523682	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv546822	chr1:94246577-94289863	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv1815663	chr1:94246577-94291252	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1877	chr1:94247756-94292908	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv508415	chr1:94256122-94305339	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2223908	GCLM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94262400-94270200	Enhancers	Hela-S3	cervix
2	chr1:94267600-94270200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:94267600-94273400	Weak transcription	Lung	lung
4	chr1:94268000-94270200	Enhancers	NHDF-Ad	bronchial
5	chr1:94268200-94270200	Enhancers	HUVEC	blood vessel
6	chr1:94268200-94271000	Weak transcription	Small Intestine	intestine
7	chr1:94268600-94271200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:94268800-94270200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:94268800-94270200	Enhancers	Muscle Satellite Cultured Cells	--
10	chr1:94268800-94271400	Enhancers	HMEC	breast
11	chr1:94269200-94270200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:94269200-94270200	Enhancers	Osteobl	bone
13	chr1:94269200-94271000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:94269200-94271200	Enhancers	NH-A	brain
15	chr1:94269200-94271600	Enhancers	NHEK	skin
16	chr1:94269200-94272000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:94269400-94270200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:94269400-94271000	Enhancers	NHLF	lung
19	chr1:94269400-94271200	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr1:94269400-94271200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:94269400-94271200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:94269400-94271200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:94269600-94270800	Weak transcription	Right Atrium	heart
24	chr1:94269800-94270200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:94269800-94270200	Weak transcription	HSMM	muscle
26	chr1:94269800-94270800	Weak transcription	Placenta	Placenta
27	chr1:94269800-94270800	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr1:94269800-94271000	Enhancers	Fetal Lung	lung
29	chr1:94269800-94273200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr1:94270000-94270400	Enhancers	Aorta	Aorta
31	chr1:94270000-94270600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:94270000-94270800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr1:94270000-94270800	Weak transcription	Left Ventricle	heart
34	chr1:94270000-94271000	Enhancers	HSMMtube	muscle
35	chr1:94270000-94271200	Flanking Active TSS	A549	lung

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