Variant report

Variant	rs6669122
Chromosome Location	chr1:150591732-150591733
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:150590845..150592459-chr1:150946616..150948291,2	MCF-7	breast:
2	chr1:150447560..150450258-chr1:150589429..150592366,2	MCF-7	breast:
3	chr1:150459071..150461984-chr1:150591178..150593029,2	MCF-7	breast:
4	chr1:150548506..150553393-chr1:150590797..150599175,18	MCF-7	breast:
5	chr1:150538995..150557554-chr1:150581886..150604495,126	K562	blood:
6	chr1:150531963..150536011-chr1:150591447..150597197,8	K562	blood:
7	chr1:150532182..150537720-chr1:150588719..150604935,28	MCF-7	breast:
8	chr1:150590724..150593722-chr1:150607408..150609980,2	K562	blood:
9	chr1:150578499..150580470-chr1:150591398..150593664,2	MCF-7	breast:
10	chr1:150590605..150592939-chr1:150782723..150785230,3	MCF-7	breast:
11	chr1:150532035..150536180-chr1:150591447..150597251,6	K562	blood:
12	chr1:150531290..150540028-chr1:150591374..150603951,29	MCF-7	breast:
13	chr1:150544010..150546916-chr1:150590925..150592477,2	MCF-7	breast:
14	chr1:150548467..150555490-chr1:150590800..150598161,17	MCF-7	breast:
15	chr1:150544073..150554289-chr1:150582699..150598712,61	K562	blood:
16	chr1:150591621..150596223-chr1:150788180..150792847,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000143384	Chromatin interaction
ENSG00000264584	Chromatin interaction
ENSG00000143437	Chromatin interaction
ENSG00000200175	Chromatin interaction
ENSG00000143418	Chromatin interaction
ENSG00000143374	Chromatin interaction
ENSG00000264508	Chromatin interaction
ENSG00000203804	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1053732	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10888384	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10888385	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11204668	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs11204669	0.81[ASN][1000 genomes]
rs11204675	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11204677	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11204678	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11204679	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11204680	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11204684	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11585169	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12125672	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12126271	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12139563	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12406712	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12746899	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1971378	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2048558	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3738484	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3738485	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3754209	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4970918	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4970923	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4971041	0.82[AFR][1000 genomes]
rs55862611	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs61820165	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6697620	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6698495	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs878471	0.81[ASN][1000 genomes]
rs9803935	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[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	nsv1006838	chr1:150440214-150722783	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs6669122	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs6669122	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs6669122	HORMAD1	cis	Esophagus Mucosa	GTEx
rs6669122	GOLPH3L	cis	Nerve Tibial	GTEx
rs6669122	CTSS	cis	Nerve Tibial	GTEx
rs6669122	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs6669122	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs6669122	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs6669122	ARNT	cis	Thyroid	GTEx
rs6669122	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs6669122	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs6669122	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs6669122	HORMAD1	cis	Nerve Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150553200-150592000	Weak transcription	Fetal Kidney	kidney
2	chr1:150578000-150592600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:150582400-150594400	Weak transcription	Ovary	ovary
4	chr1:150582600-150591800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:150584400-150594800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:150584400-150600600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:150584800-150594400	Weak transcription	Gastric	stomach
8	chr1:150584800-150596200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:150584800-150600200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:150585000-150600000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:150585200-150600200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr1:150585400-150594200	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr1:150586200-150591800	Weak transcription	Colon Smooth Muscle	Colon
14	chr1:150586200-150594600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:150586400-150592200	Weak transcription	Aorta	Aorta
16	chr1:150586400-150592200	Weak transcription	Brain Substantia Nigra	brain
17	chr1:150586600-150591800	Weak transcription	Brain Angular Gyrus	brain
18	chr1:150586600-150591800	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr1:150586600-150592000	Strong transcription	Fetal Stomach	stomach
20	chr1:150586600-150592600	Weak transcription	Right Atrium	heart
21	chr1:150586600-150600400	Strong transcription	Fetal Muscle Trunk	muscle
22	chr1:150586800-150591800	Weak transcription	Stomach Smooth Muscle	stomach
23	chr1:150586800-150592200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr1:150587000-150591800	Weak transcription	Primary B cells from cord blood	blood
25	chr1:150587000-150592000	Weak transcription	Brain Hippocampus Middle	brain
26	chr1:150587000-150592000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr1:150587000-150592800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr1:150587200-150591800	Weak transcription	NHDF-Ad	bronchial
29	chr1:150587200-150592000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr1:150587200-150594400	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr1:150587200-150594600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:150587600-150592200	Strong transcription	Primary B cells from peripheral blood	blood
33	chr1:150587600-150592400	Strong transcription	Fetal Muscle Leg	muscle
34	chr1:150587600-150592800	Strong transcription	Placenta	Placenta
35	chr1:150587800-150594200	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr1:150587800-150596200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr1:150587800-150598800	Strong transcription	Dnd41	blood
38	chr1:150587800-150600000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr1:150587800-150600400	Strong transcription	Brain Germinal Matrix	brain
40	chr1:150588000-150592000	Weak transcription	Liver	Liver
41	chr1:150588000-150592000	Strong transcription	Fetal Intestine Small	intestine
42	chr1:150588000-150592400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr1:150588000-150592400	Weak transcription	Stomach Mucosa	stomach
44	chr1:150588200-150592000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:150588200-150592200	Strong transcription	Brain Cingulate Gyrus	brain
46	chr1:150588200-150594000	Strong transcription	Fetal Thymus	thymus
47	chr1:150588200-150595200	Weak transcription	Spleen	Spleen
48	chr1:150588200-150600200	Strong transcription	Fetal Intestine Large	intestine
49	chr1:150588400-150591800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr1:150588600-150591800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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