Variant report

Variant	rs17878271
Chromosome Location	chr1:94361182-94361183
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	chr1:94360896..94362879-chr1:94374618..94376301,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000023909	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10489605	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10874795	0.81[ASN][1000 genomes]
rs11164994	0.85[EUR][1000 genomes]
rs11165019	0.81[ASN][1000 genomes]
rs12079584	0.81[ASN][1000 genomes]
rs12239830	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17100397	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17304770	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17878294	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17881810	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17884788	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17885151	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17886352	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2223908	0.87[EUR][1000 genomes]
rs3761913	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41292665	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57870303	0.85[EUR][1000 genomes]
rs61425457	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61781049	0.83[EUR][1000 genomes]
rs61781051	0.85[EUR][1000 genomes]
rs61781053	0.87[EUR][1000 genomes]
rs61781054	0.85[EUR][1000 genomes]
rs61781055	0.85[EUR][1000 genomes]
rs61781056	0.85[EUR][1000 genomes]
rs61781057	0.87[EUR][1000 genomes]
rs61782162	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61782163	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61782164	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61782165	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61782167	0.86[ASN][1000 genomes]
rs61782398	0.85[EUR][1000 genomes]
rs61782399	0.85[EUR][1000 genomes]
rs61782400	0.87[EUR][1000 genomes]
rs61782403	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61782404	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61782405	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61782410	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61782413	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61782449	0.88[EUR][1000 genomes]
rs61782450	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61782451	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61782458	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61782459	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6674149	0.80[EUR][1000 genomes]
rs72723114	0.85[EUR][1000 genomes]
rs72723118	0.86[EUR][1000 genomes]
rs72723125	0.87[EUR][1000 genomes]
rs72723138	0.85[EUR][1000 genomes]
rs72723157	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72723165	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72723169	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72723178	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72723192	0.94[ASN][1000 genomes]
rs72967397	0.81[ASN][1000 genomes]
rs7523682	0.83[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523355	chr1:94351328-94385591	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17878271	GCLM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94345000-94374200	Weak transcription	Gastric	stomach
2	chr1:94345000-94374200	Weak transcription	Spleen	Spleen
3	chr1:94345200-94374000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:94345200-94374200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:94345400-94362000	Weak transcription	Fetal Muscle Leg	muscle
6	chr1:94345400-94364000	Weak transcription	Fetal Intestine Small	intestine
7	chr1:94345400-94369400	Weak transcription	Colonic Mucosa	Colon
8	chr1:94345400-94373200	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr1:94345400-94373200	Weak transcription	Brain Substantia Nigra	brain
10	chr1:94345400-94373800	Weak transcription	Fetal Stomach	stomach
11	chr1:94345400-94374000	Weak transcription	Right Ventricle	heart
12	chr1:94345600-94361800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr1:94345600-94362000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr1:94345600-94362000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr1:94345600-94362000	Weak transcription	Brain Hippocampus Middle	brain
16	chr1:94345600-94369400	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr1:94345600-94369400	Weak transcription	Fetal Lung	lung
18	chr1:94345600-94369800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr1:94345600-94371600	Weak transcription	Fetal Kidney	kidney
20	chr1:94345600-94373000	Weak transcription	Fetal Brain Female	brain
21	chr1:94345600-94373200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr1:94345600-94373200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr1:94345600-94373200	Weak transcription	Fetal Brain Male	brain
24	chr1:94345600-94373400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr1:94345600-94373400	Weak transcription	Psoas Muscle	Psoas
26	chr1:94345600-94373400	Weak transcription	Stomach Mucosa	stomach
27	chr1:94345600-94373600	Weak transcription	Brain Germinal Matrix	brain
28	chr1:94345800-94362000	Weak transcription	HSMMtube	muscle
29	chr1:94345800-94366000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr1:94345800-94369200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr1:94345800-94371200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr1:94347400-94374200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:94347600-94367600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr1:94350400-94367200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr1:94350600-94369400	Strong transcription	HMEC	breast
36	chr1:94351200-94364600	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr1:94351200-94367400	Strong transcription	Liver	Liver
38	chr1:94351600-94362000	Weak transcription	Ovary	ovary
39	chr1:94352800-94370400	Weak transcription	Lung	lung
40	chr1:94352800-94373000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:94353000-94361800	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr1:94353000-94367400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:94353600-94363400	Strong transcription	Dnd41	blood
44	chr1:94353600-94367200	Strong transcription	Osteobl	bone
45	chr1:94353600-94368200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr1:94353800-94367200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:94354200-94370400	Weak transcription	Small Intestine	intestine
48	chr1:94354200-94372600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr1:94354400-94367000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:94354600-94367000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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