Variant report

Variant	rs708126
Chromosome Location	chr1:228283876-228283877
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:32)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:32 , 50 per page) page: 1

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	chr1:228283656-228283972	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr1:228283602-228288407	K562	blood:	n/a	n/a
4	POLR2A	chr1:228283620-228284039	GM12878	blood:	n/a	n/a
5	POLR2A	chr1:228282889-228288572	GM12878	blood:	n/a	n/a
6	POLR2A	chr1:228283138-228288342	GM12892	blood:	n/a	n/a
7	POLR2A	chr1:228283711-228284110	MCF-7	breast:	n/a	n/a
8	POLR2A	chr1:228283629-228284474	U87	brain:	n/a	n/a
9	POLR2A	chr1:228283824-228288153	K562	blood:	n/a	n/a
10	POLR2A	chr1:228282920-228289800	GM12878	blood:	n/a	n/a
11	POLR2A	chr1:228283571-228285986	GM12891	blood:	n/a	n/a
12	MAFK	chr1:228283863-228283884	K562	blood:	n/a	n/a
13	POLR2A	chr1:228283284-228284619	K562	blood:	n/a	n/a
14	POLR2A	chr1:228283616-228283877	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr1:228283628-228284317	U87	brain:	n/a	n/a
16	POLR2A	chr1:228283300-228288960	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr1:228283783-228289635	K562	blood:	n/a	n/a
18	POLR2A	chr1:228283072-228285818	GM19193	blood:	n/a	n/a
19	POLR2A	chr1:228274170-228289426	HepG2	liver:	n/a	n/a
20	POLR2A	chr1:228283248-228289096	GM12892	blood:	n/a	n/a
21	POLR2A	chr1:228283873-228285780	A549	lung:	n/a	n/a
22	POLR2A	chr1:228283647-228285922	GM12891	blood:	n/a	n/a
23	POLR2A	chr1:228282873-228290384	GM12878	blood:	n/a	n/a
24	POLR2A	chr1:228283623-228283900	HUVEC	blood vessel:	n/a	n/a
25	POLR2A	chr1:228283726-228293977	K562	blood:	n/a	n/a
26	POLR2A	chr1:228283870-228284911	HepG2	liver:	n/a	n/a
27	POLR2A	chr1:228283134-228289712	GM12878	blood:	n/a	n/a
28	POLR2A	chr1:228283751-228283999	HepG2	liver:	n/a	n/a
29	POLR2A	chr1:228283698-228283889	GM12878	blood:	n/a	n/a
30	POLR2A	chr1:228283846-228290152	PFSK-1	brain:	n/a	n/a
31	CTCF	chr1:228283800-228283950	SAEC	small airway:	n/a	chr1:228283909-228283918
32	FOS	chr1:228283798-228283929	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

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

No data

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

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1034792	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1048503	1.00[CEU][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes]
rs10916261	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1094602	0.82[ASN][1000 genomes]
rs11582265	0.91[EUR][1000 genomes]
rs11582704	0.91[EUR][1000 genomes]
rs11584499	0.86[JPT][hapmap]
rs1188975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1188977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13374948	0.84[CHB][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1620734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1745420	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2070960	0.93[EUR][1000 genomes]
rs2107905	0.86[ASN][1000 genomes]
rs2295995	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3738680	1.00[CEU][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes]
rs3738681	1.00[CEU][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes]
rs3768329	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs3768330	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs3820624	0.91[EUR][1000 genomes]
rs41270177	0.99[ASN][1000 genomes]
rs4653533	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4653897	0.97[ASN][1000 genomes]
rs4653906	0.93[CHB][hapmap]
rs61825135	0.84[EUR][1000 genomes]
rs6668719	0.85[CHB][hapmap]
rs7537552	0.92[CHB][hapmap];0.81[ASN][1000 genomes]
rs7539664	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs822727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs860301	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[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

No data

Chromatin state (count:125 , 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	chr1:228279000-228285000	Weak transcription	HSMMtube	muscle
11	chr1:228279200-228287800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:228279400-228284200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:228279600-228285600	Weak transcription	NH-A	brain
14	chr1:228279600-228289000	Strong transcription	Muscle Satellite Cultured Cells	--
15	chr1:228280000-228284000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr1:228280000-228284000	ZNF genes & repeats	Fetal Thymus	thymus
17	chr1:228280000-228284200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:228280000-228285200	ZNF genes & repeats	Fetal Stomach	stomach
19	chr1:228280200-228284400	ZNF genes & repeats	Fetal Brain Female	brain
20	chr1:228280200-228288800	Weak transcription	Fetal Heart	heart
21	chr1:228280400-228285400	ZNF genes & repeats	Brain Germinal Matrix	brain
22	chr1:228280600-228286400	Weak transcription	Psoas Muscle	Psoas
23	chr1:228280800-228289600	Weak transcription	Small Intestine	intestine
24	chr1:228281000-228284000	Strong transcription	Stomach Smooth Muscle	stomach
25	chr1:228281200-228284200	Weak transcription	Colon Smooth Muscle	Colon
26	chr1:228281400-228289000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:228282400-228284200	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr1:228282400-228284200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr1:228282400-228284600	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr1:228282400-228289200	Strong transcription	NHEK	skin
31	chr1:228282600-228284000	Weak transcription	Rectal Smooth Muscle	rectum
32	chr1:228282600-228284200	Weak transcription	Duodenum Mucosa	Duodenum
33	chr1:228282600-228284600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr1:228282600-228285000	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr1:228282600-228285200	Weak transcription	HMEC	breast
36	chr1:228282600-228285600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:228282600-228286400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr1:228282600-228287200	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr1:228282600-228288800	Strong transcription	K562	blood
40	chr1:228282600-228289000	Strong transcription	Primary T cells from cord blood	blood
41	chr1:228282800-228284000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr1:228282800-228284000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr1:228282800-228284200	Genic enhancers	Osteobl	bone
44	chr1:228282800-228284400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr1:228282800-228284600	Genic enhancers	Primary T cells fromperipheralblood	blood
46	chr1:228282800-228284600	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr1:228282800-228285000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr1:228282800-228285200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr1:228282800-228285200	Weak transcription	HUVEC	blood vessel
50	chr1:228282800-228287400	Strong transcription	GM12878-XiMat	blood

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