Variant report

Variant	rs6680315
Chromosome Location	chr1:94370519-94370520
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:94366538..94368489-chr1:94369960..94371845,2	MCF-7	breast:
2	chr1:94340990..94343514-chr1:94369991..94373741,3	K562	blood:
3	chr1:94368166..94370770-chr1:94373424..94375142,2	MCF-7	breast:
4	chr1:94370087..94372566-chr1:94373448..94376204,3	MCF-7	breast:
5	chr1:94342014..94348814-chr1:94369991..94376733,14	K562	blood:

Variant related genes	Relation type
ENSG00000023909	Chromatin interaction
ENSG00000067334	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10874808	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10874809	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11165030	0.82[ASN][1000 genomes]
rs2064764	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2391323	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3170633	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3761912	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6667121	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6687387	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6689601	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7513671	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7515191	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7517826	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7533596	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7549683	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6680315	GCLM	Cis_1M	lymphoblastoid	RTeQTL
rs6680315	GCLM	cis	Thyroid	GTEx

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	chr1:94345400-94373200	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr1:94345400-94373200	Weak transcription	Brain Substantia Nigra	brain
7	chr1:94345400-94373800	Weak transcription	Fetal Stomach	stomach
8	chr1:94345400-94374000	Weak transcription	Right Ventricle	heart
9	chr1:94345600-94371600	Weak transcription	Fetal Kidney	kidney
10	chr1:94345600-94373000	Weak transcription	Fetal Brain Female	brain
11	chr1:94345600-94373200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr1:94345600-94373200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:94345600-94373200	Weak transcription	Fetal Brain Male	brain
14	chr1:94345600-94373400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:94345600-94373400	Weak transcription	Psoas Muscle	Psoas
16	chr1:94345600-94373400	Weak transcription	Stomach Mucosa	stomach
17	chr1:94345600-94373600	Weak transcription	Brain Germinal Matrix	brain
18	chr1:94345800-94371200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:94347400-94374200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:94352800-94373000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:94354200-94372600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr1:94354600-94373400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr1:94356600-94372600	Weak transcription	Colon Smooth Muscle	Colon
24	chr1:94357200-94373800	Weak transcription	Thymus	Thymus
25	chr1:94357400-94374000	Weak transcription	Aorta	Aorta
26	chr1:94357600-94374200	Weak transcription	Pancreas	Pancrea
27	chr1:94357800-94373200	Weak transcription	Esophagus	oesophagus
28	chr1:94357800-94374000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr1:94359800-94373800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr1:94359800-94374000	Weak transcription	Fetal Muscle Trunk	muscle
31	chr1:94360400-94373200	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr1:94360800-94373000	Weak transcription	Fetal Heart	heart
33	chr1:94362400-94373200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:94362400-94373200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr1:94362400-94373200	Weak transcription	Brain Angular Gyrus	brain
36	chr1:94362600-94373200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:94362600-94373400	Weak transcription	Stomach Smooth Muscle	stomach
38	chr1:94362600-94373800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr1:94362600-94374200	Weak transcription	Left Ventricle	heart
40	chr1:94362800-94372000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr1:94362800-94373000	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr1:94362800-94373200	Weak transcription	Fetal Muscle Leg	muscle
43	chr1:94362800-94373400	Weak transcription	Fetal Thymus	thymus
44	chr1:94362800-94374000	Weak transcription	Ovary	ovary
45	chr1:94363000-94373200	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr1:94363400-94370800	Weak transcription	NHLF	lung
47	chr1:94363400-94373200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr1:94364400-94371000	Weak transcription	Fetal Intestine Small	intestine
49	chr1:94366200-94373400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr1:94366800-94374000	Weak transcription	Sigmoid Colon	Sigmoid Colon

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