Variant report

Variant	rs2292481
Chromosome Location	chr1:212640333-212640334
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212639292..212640942-chr1:212781990..212784541,2	K562	blood:
2	chr1:212639889..212643172-chr1:212795709..212798826,3	K562	blood:
3	chr1:212639121..212641967-chr1:212780550..212783593,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM206-2	chr1:212640158-212640439	XLOC_001193

Variant related genes	Relation type
ENSG00000162771	Chromatin interaction
ENSG00000162772	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12131037	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12135668	0.83[ASN][1000 genomes]
rs12729438	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12753186	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12754528	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13374785	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2005230	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2292479	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292482	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001262	0.82[EUR][1000 genomes]
rs34543166	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs36056520	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3951316	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs525176	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs557252	0.82[EUR][1000 genomes]
rs591176	0.82[ASN][1000 genomes]
rs624387	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs626178	0.82[EUR][1000 genomes]
rs638527	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs653006	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs653532	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6669813	0.86[ASN][1000 genomes]
rs6704297	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs679840	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7513550	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7517259	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7519767	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7529867	0.86[ASN][1000 genomes]
rs7553229	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs796930	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs806539	0.83[ASN][1000 genomes]
rs902438	0.82[ASN][1000 genomes]
rs902439	0.84[ASN][1000 genomes]
rs9430096	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
6	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
7	nsv873156	chr1:212585092-212646225	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv873157	chr1:212610755-212640982	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv873158	chr1:212610755-212646225	Weak transcription Strong transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv873159	chr1:212610755-212669475	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv873160	chr1:212610755-212675482	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv873161	chr1:212610755-212683565	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv873162	chr1:212610755-212716033	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv527863	chr1:212617423-212700618	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv873163	chr1:212629935-212669475	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2292481	C1orf75	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212629800-212642600	Weak transcription	Stomach Smooth Muscle	stomach
2	chr1:212629800-212643200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr1:212635600-212641800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:212635800-212640600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr1:212635800-212641400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:212636400-212641000	Weak transcription	Brain Angular Gyrus	brain
7	chr1:212636600-212643200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:212636800-212641600	Enhancers	Placenta Amnion	Placenta Amnion
9	chr1:212636800-212644400	Enhancers	Placenta	Placenta
10	chr1:212637000-212640400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr1:212637600-212644800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:212637800-212640400	Weak transcription	Brain Anterior Caudate	brain
13	chr1:212638200-212640800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr1:212638200-212643400	Weak transcription	Spleen	Spleen
15	chr1:212638600-212640400	Weak transcription	NHEK	skin
16	chr1:212638600-212643200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr1:212638800-212641000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr1:212638800-212641200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:212639000-212640400	Enhancers	Esophagus	oesophagus
20	chr1:212639800-212640400	Enhancers	K562	blood
21	chr1:212639800-212641800	Enhancers	Brain Substantia Nigra	brain
22	chr1:212639800-212642000	Enhancers	Brain Cingulate Gyrus	brain
23	chr1:212640000-212640600	Enhancers	Fetal Muscle Trunk	muscle
24	chr1:212640000-212640600	Enhancers	Pancreas	Pancrea
25	chr1:212640000-212641600	Enhancers	Brain Hippocampus Middle	brain
26	chr1:212640000-212641600	Enhancers	Fetal Muscle Leg	muscle
27	chr1:212640000-212641800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr1:212640000-212641800	Enhancers	Fetal Lung	lung
29	chr1:212640200-212640400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr1:212640200-212640400	Enhancers	Left Ventricle	heart
31	chr1:212640200-212640400	Enhancers	Right Atrium	heart
32	chr1:212640200-212641000	Enhancers	Fetal Intestine Large	intestine
33	chr1:212640200-212641200	Enhancers	Fetal Kidney	kidney
34	chr1:212640200-212641200	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr1:212640200-212641400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr1:212640200-212641800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links