Variant report

Variant	rs2427
Chromosome Location	chr8:8641125-8641126
allele	C/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	ZNF384	chr8:8640971-8641245	GM12878	blood:	n/a	n/a
2	EP300	chr8:8641085-8641285	GM12878	blood:	n/a	n/a
3	SPI1	chr8:8641025-8641299	HL-60	blood:	n/a	n/a
4	RUNX3	chr8:8640884-8641353	GM12878	blood:	n/a	chr8:8640935-8640944 chr8:8640935-8640944
5	RUNX3	chr8:8640929-8641296	GM12878	blood:	n/a	chr8:8640935-8640944 chr8:8640935-8640944
6	POLR2A	chr8:8640814-8641337	HUVEC	blood vessel:	n/a	n/a
7	FOS	chr8:8640969-8641454	HUVEC	blood vessel:	n/a	n/a
8	SPI1	chr8:8640900-8641273	HL-60	blood:	n/a	n/a
9	GATA2	chr8:8640979-8641262	HUVEC	blood vessel:	n/a	chr8:8640982-8640991
10	STAT3	chr8:8640967-8641236	MCF10A-Er-Src	breast:	n/a	chr8:8641117-8641137 chr8:8641120-8641134 chr8:8641116-8641137 chr8:8641122-8641131 chr8:8641076-8641087 chr8:8641123-8641132 chr8:8641121-8641132 chr8:8641156-8641167
11	STAT3	chr8:8641063-8641143	MCF10A-Er-Src	breast:	n/a	chr8:8641117-8641137 chr8:8641120-8641134 chr8:8641116-8641137 chr8:8641122-8641131 chr8:8641076-8641087 chr8:8641123-8641132 chr8:8641121-8641132
12	STAT3	chr8:8641013-8641257	MCF10A-Er-Src	breast:	n/a	chr8:8641117-8641137 chr8:8641120-8641134 chr8:8641116-8641137 chr8:8641122-8641131 chr8:8641076-8641087 chr8:8641123-8641132 chr8:8641121-8641132 chr8:8641156-8641167

No.	Distal block	Cell Line	Cell type
1	chr8:8637079..8641758-chr8:8747812..8752273,5	MCF-7	breast:
2	chr8:8635419..8638505-chr8:8640387..8644598,4	K562	blood:
3	chr8:8640474..8642635-chr8:8745832..8748288,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254367	TF binding region
ENSG00000147324	Chromatin interaction

Extended variants
information (count: 114 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10089188	0.90[EUR][1000 genomes]
rs10092600	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10092720	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10093872	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10094270	0.84[ASN][1000 genomes]
rs10098636	0.84[ASN][1000 genomes]
rs10105690	0.84[ASN][1000 genomes]
rs10105920	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10109886	1.00[JPT][hapmap]
rs10112989	0.84[ASN][1000 genomes]
rs10113326	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1039910	0.84[ASN][1000 genomes]
rs1039911	0.84[ASN][1000 genomes]
rs1039912	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10503392	0.87[ASN][1000 genomes]
rs11774722	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11774744	0.87[ASN][1000 genomes]
rs11774860	0.82[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap]
rs11775476	0.80[ASN][1000 genomes]
rs11775821	0.87[ASN][1000 genomes]
rs11775888	0.87[ASN][1000 genomes]
rs11776440	0.86[AMR][1000 genomes]
rs11776513	0.87[ASN][1000 genomes]
rs11776546	0.87[ASN][1000 genomes]
rs11776845	0.83[ASN][1000 genomes]
rs11777091	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11778970	0.87[ASN][1000 genomes]
rs11779327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11779524	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11780216	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11780824	0.91[ASN][1000 genomes]
rs11781542	0.87[ASN][1000 genomes]
rs11781841	0.91[ASN][1000 genomes]
rs11782235	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11783112	0.87[ASN][1000 genomes]
rs11783944	0.86[ASN][1000 genomes]
rs11783950	0.86[ASN][1000 genomes]
rs11784958	0.87[ASN][1000 genomes]
rs11786455	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11906	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11985640	0.81[CEU][hapmap];0.88[GIH][hapmap]
rs11987146	0.84[ASN][1000 genomes]
rs11987904	0.84[ASN][1000 genomes]
rs11987924	0.84[ASN][1000 genomes]
rs11997731	0.84[ASN][1000 genomes]
rs11997763	0.84[ASN][1000 genomes]
rs12155530	0.87[ASN][1000 genomes]
rs1589613	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17154702	0.87[ASN][1000 genomes]
rs17154709	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs17154743	0.82[CEU][hapmap];0.88[GIH][hapmap]
rs17629935	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17630714	0.82[CEU][hapmap]
rs17631022	0.82[CEU][hapmap]
rs17631052	0.82[CEU][hapmap];0.88[GIH][hapmap]
rs17698256	0.82[CEU][hapmap];0.88[GIH][hapmap]
rs28402110	0.84[ASN][1000 genomes]
rs28521727	0.84[ASN][1000 genomes]
rs28583936	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34473848	0.84[ASN][1000 genomes]
rs34732488	0.84[ASN][1000 genomes]
rs35457364	0.84[ASN][1000 genomes]
rs35654766	0.83[ASN][1000 genomes]
rs3748142	0.82[CEU][hapmap]
rs3748143	0.82[CEU][hapmap];0.88[GIH][hapmap]
rs3827807	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3827812	0.82[CEU][hapmap];0.88[GIH][hapmap]
rs4840356	0.87[ASN][1000 genomes]
rs4840359	1.00[ASN][1000 genomes]
rs4840365	0.83[ASN][1000 genomes]
rs4841030	0.87[ASN][1000 genomes]
rs4841031	0.87[ASN][1000 genomes]
rs55816468	0.87[ASN][1000 genomes]
rs55874147	0.91[ASN][1000 genomes]
rs55971558	0.87[ASN][1000 genomes]
rs56007835	0.87[ASN][1000 genomes]
rs56152067	0.91[ASN][1000 genomes]
rs56173033	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56188408	0.91[ASN][1000 genomes]
rs57301822	0.87[ASN][1000 genomes]
rs66564323	0.83[ASN][1000 genomes]
rs66618176	0.80[ASN][1000 genomes]
rs67000451	0.83[ASN][1000 genomes]
rs67653033	0.83[ASN][1000 genomes]
rs67766414	0.84[ASN][1000 genomes]
rs7002397	1.00[CHB][hapmap]
rs73198272	0.87[ASN][1000 genomes]
rs73198279	0.87[ASN][1000 genomes]
rs73198286	0.87[ASN][1000 genomes]
rs73198287	0.87[ASN][1000 genomes]
rs73198288	0.87[ASN][1000 genomes]
rs73198290	0.87[ASN][1000 genomes]
rs73201840	0.91[ASN][1000 genomes]
rs7813355	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7820324	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs964773	0.80[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv890331	chr8:8093240-8971100	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers 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	43 gene(s)	inside rSNPs	diseases
2	nsv1030433	chr8:8130629-8653691	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv539447	chr8:8130629-8653691	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv1033463	chr8:8221922-8674333	Weak transcription Bivalent/Poised TSS Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv539451	chr8:8221922-8674333	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv1019606	chr8:8353661-8736992	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv539456	chr8:8353661-8736992	Strong transcription Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv995047	chr8:8353662-8857913	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv1022511	chr8:8493992-8737132	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
10	nsv539457	chr8:8493992-8737132	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
11	esv1795023	chr8:8583943-8655580	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
12	esv1825234	chr8:8583943-8655580	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
13	esv1824870	chr8:8583943-8699382	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
14	nsv610189	chr8:8590437-8664940	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
15	nsv831228	chr8:8608387-8790790	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
16	nsv1018828	chr8:8609880-8790660	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
17	nsv1022331	chr8:8610035-8787981	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats 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	4 gene(s)	inside rSNPs	diseases
18	nsv917117	chr8:8621658-9313799	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2427	TDH	cis	cerebellum	SCAN
rs2427	MFHAS1	cis	cerebellum	SCAN
rs2427	ENO2	trans	parietal	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:8621400-8646200	Weak transcription	Right Atrium	heart
2	chr8:8630600-8642200	Weak transcription	Fetal Brain Female	brain
3	chr8:8630800-8641200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr8:8630800-8646400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr8:8630800-8647400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr8:8631000-8641200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr8:8631000-8642000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr8:8631000-8646400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr8:8631000-8647200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr8:8631000-8648400	Weak transcription	Fetal Stomach	stomach
11	chr8:8631200-8641200	Weak transcription	Aorta	Aorta
12	chr8:8631200-8652400	Weak transcription	Ovary	ovary
13	chr8:8633200-8641200	Weak transcription	HSMMtube	muscle
14	chr8:8633800-8641800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr8:8637400-8641200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr8:8637600-8642000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr8:8637600-8646000	Weak transcription	Left Ventricle	heart
18	chr8:8637600-8646200	Weak transcription	Pancreas	Pancrea
19	chr8:8637600-8648800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr8:8637600-8653400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr8:8637600-8679800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr8:8637800-8641600	Weak transcription	Fetal Brain Male	brain
23	chr8:8637800-8642400	Weak transcription	Colon Smooth Muscle	Colon
24	chr8:8637800-8648000	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr8:8637800-8651000	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr8:8638000-8641200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr8:8638000-8641200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr8:8638000-8646200	Weak transcription	K562	blood
29	chr8:8638200-8651000	Weak transcription	Fetal Intestine Large	intestine
30	chr8:8638400-8641600	Weak transcription	Fetal Heart	heart
31	chr8:8638600-8641200	Weak transcription	Primary B cells from cord blood	blood
32	chr8:8639000-8646600	Weak transcription	Brain Germinal Matrix	brain
33	chr8:8639600-8641200	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr8:8639600-8641600	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr8:8639600-8641600	Enhancers	Fetal Thymus	thymus
36	chr8:8639600-8641600	Enhancers	Spleen	Spleen
37	chr8:8639600-8641800	Enhancers	Primary hematopoietic stem cells	blood
38	chr8:8639600-8641800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr8:8639600-8641800	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr8:8639600-8642000	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr8:8639800-8641200	Enhancers	Primary T cells from cord blood	blood
42	chr8:8639800-8641400	Enhancers	Fetal Muscle Leg	muscle
43	chr8:8639800-8641600	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr8:8639800-8641600	Enhancers	Primary T killer memory cells from peripheral blood	blood
45	chr8:8639800-8641600	Enhancers	Adipose Nuclei	Adipose
46	chr8:8639800-8641600	Enhancers	Liver	Liver
47	chr8:8639800-8641600	Enhancers	Monocytes-CD14+_RO01746	blood
48	chr8:8639800-8646200	Weak transcription	Right Ventricle	heart
49	chr8:8640000-8641200	Enhancers	Muscle Satellite Cultured Cells	--
50	chr8:8640000-8641200	Enhancers	Fetal Lung	lung

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