Variant report

Variant	rs822725
Chromosome Location	chr1:228282877-228282878
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:228274276-228290284	K562	blood:	n/a	n/a
2	POLR2A	chr1:228274170-228289426	HepG2	liver:	n/a	n/a
3	POLR2A	chr1:228281686-228283098	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr1:228282873-228290384	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:228281021..228283258-chr1:228327400..228329608,2	MCF-7	breast:
2	chr1:228281446..228284269-chr1:228337109..228339071,2	K562	blood:
3	chr1:228282033..228284613-chr1:228342310..228344410,2	MCF-7	breast:

Variant related genes	Relation type
MIR3620	TF binding region
ENSG00000143774	Chromatin interaction
ENSG00000198835	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12084338	0.82[TSI][hapmap]
rs12134624	0.83[GIH][hapmap];0.82[TSI][hapmap]
rs28634124	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3121310	1.00[CEU][hapmap];0.89[GIH][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs4653917	0.83[GIH][hapmap];0.82[TSI][hapmap]
rs6426492	0.94[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.81[ASN][1000 genomes]
rs6682260	0.83[GIH][hapmap];0.82[TSI][hapmap]
rs708123	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs752107	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7523917	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7539762	0.83[GIH][hapmap];0.82[TSI][hapmap]
rs766972	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs822733	0.80[EUR][1000 genomes]
rs822739	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs822740	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs849749	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
5	nsv516409	chr1:228035131-228296745	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
7	nsv832803	chr1:228155118-228313681	Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
9	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
10	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
11	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs822725	ITPKB	cis	cerebellum	SCAN
rs822725	ACBD3	cis	cerebellum	SCAN
rs822725	C1orf69	cis	cerebellum	SCAN
rs822725	OBSCN	cis	Esophagus Mucosa	GTEx
rs822725	WDR26	cis	cerebellum	SCAN
rs822725	TMEM63A	cis	cerebellum	SCAN
rs822725	GUK1	cis	parietal	SCAN
rs822725	OBSCN	cis	Skin Sun Exposed Lower leg	GTEx
rs822725	MRPL55	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228272400-228284400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:228273000-228284200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr1:228273400-228285200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr1:228275800-228286600	Weak transcription	Fetal Kidney	kidney
5	chr1:228276600-228285000	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr1:228276800-228290200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:228277200-228290000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:228277600-228289200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:228278000-228289400	Genic enhancers	Pancreas	Pancrea
10	chr1:228278800-228283000	ZNF genes & repeats	Dnd41	blood
11	chr1:228278800-228283600	Weak transcription	Ovary	ovary
12	chr1:228279000-228285000	Weak transcription	HSMMtube	muscle
13	chr1:228279200-228287800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr1:228279400-228283400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr1:228279400-228284200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:228279600-228285600	Weak transcription	NH-A	brain
17	chr1:228279600-228289000	Strong transcription	Muscle Satellite Cultured Cells	--
18	chr1:228280000-228283600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:228280000-228283600	ZNF genes & repeats	Thymus	Thymus
20	chr1:228280000-228284000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:228280000-228284000	ZNF genes & repeats	Fetal Thymus	thymus
22	chr1:228280000-228284200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:228280000-228285200	ZNF genes & repeats	Fetal Stomach	stomach
24	chr1:228280200-228283200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
25	chr1:228280200-228283400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
26	chr1:228280200-228284400	ZNF genes & repeats	Fetal Brain Female	brain
27	chr1:228280200-228288800	Weak transcription	Fetal Heart	heart
28	chr1:228280400-228283400	ZNF genes & repeats	A549	lung
29	chr1:228280400-228283600	ZNF genes & repeats	Fetal Muscle Leg	muscle
30	chr1:228280400-228285400	ZNF genes & repeats	Brain Germinal Matrix	brain
31	chr1:228280600-228283800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:228280600-228286400	Weak transcription	Psoas Muscle	Psoas
33	chr1:228280800-228283400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr1:228280800-228289600	Weak transcription	Small Intestine	intestine
35	chr1:228281000-228283000	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr1:228281000-228283200	ZNF genes & repeats	Fetal Intestine Large	intestine
37	chr1:228281000-228283400	ZNF genes & repeats	Fetal Muscle Trunk	muscle
38	chr1:228281000-228283400	ZNF genes & repeats	NHLF	lung
39	chr1:228281000-228283600	ZNF genes & repeats	Fetal Intestine Small	intestine
40	chr1:228281000-228284000	Strong transcription	Stomach Smooth Muscle	stomach
41	chr1:228281200-228283200	Weak transcription	Gastric	stomach
42	chr1:228281200-228283400	Weak transcription	Stomach Mucosa	stomach
43	chr1:228281200-228283800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:228281200-228284200	Weak transcription	Colon Smooth Muscle	Colon
45	chr1:228281400-228283000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr1:228281400-228283400	Weak transcription	Right Ventricle	heart
47	chr1:228281400-228283600	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr1:228281400-228289000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:228281600-228283400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr1:228281600-228283800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links