Variant report

Variant	rs7838335
Chromosome Location	chr8:10589913-10589914
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SUZ12	chr8:10588365-10591223	H1-hESC	embryonic stem cell:	n/a	n/a
2	E2F6	chr8:10589815-10590989	H1-hESC	embryonic stem cell:	n/a	chr8:10590265-10590272 chr8:10589954-10589961 chr8:10590265-10590272 chr8:10589954-10589961 chr8:10590265-10590272 chr8:10589954-10589961 chr8:10590510-10590520
3	SUZ12	chr8:10586843-10591366	NT2-D1	testis:	n/a	n/a
4	TBP	chr8:10589767-10590154	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTBP2	chr8:10588662-10591163	H1-hESC	embryonic stem cell:	n/a	n/a
6	RAD21	chr8:10589880-10590676	H1-hESC	embryonic stem cell:	n/a	chr8:10590172-10590191
7	CTCF	chr8:10589880-10590757	A549	lung:	n/a	chr8:10590625-10590635 chr8:10590624-10590637 chr8:10590171-10590189

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr8:10589905-10589955	HRPEpiC	eye:	n/a
2	chr8:10589905-10589955	LNCaP	prostate:	n/a
3	chr8:10589905-10589955	PFSK-1	brain:	n/a
4	chr8:10589905-10589955	BE2_C	brain:	n/a
5	chr8:10589905-10589955	HepG2	liver:	n/a
6	chr8:10589905-10589955	HRE	kidney:	n/a
7	chr8:10589905-10589955	AG04450	lung:	fetal
8	chr8:10589905-10589955	HEEpiC	esophagus:	n/a
9	chr8:10589905-10589955	HIPEpiC	eye:	n/a
10	chr8:10589905-10589955	HAEpiC	amniotic membrane:	n/a
11	chr8:10589905-10589955	AoSMC	blood vessel:	n/a
12	chr8:10589905-10589955	HUVEC	blood vessel:	n/a
13	chr8:10589905-10589955	SAEC	small airway:	n/a
14	chr8:10589905-10589955	GM06990	blood:	n/a
15	chr8:10589905-10589955	AG04449	skin:	fetal
16	chr8:10589905-10589955	PrEC	prostate:	n/a
17	chr8:10589905-10589955	CMK	blood:	n/a
18	chr8:10589905-10589955	HL-60	blood:	n/a
19	chr8:10589905-10589955	GM12891	blood:	n/a
20	chr8:10589905-10589955	HCF	heart:	n/a
21	chr8:10589905-10589955	AG09319	gingival:	n/a
22	chr8:10589905-10589955	NHDF-neo	bronchial:	n/a
23	chr8:10589905-10589955	RPTEC	kidney:	n/a
24	chr8:10589905-10589955	HMEC	breast:	n/a
25	chr8:10589905-10589955	SKMC	muscle:	n/a
26	chr8:10589905-10589955	HNPCEpiC	eye:	n/a
27	chr8:10589905-10589955	GM12892	blood:	n/a
28	chr8:10589905-10589955	ECC-1	luminal epithelium:	n/a
29	chr8:10589905-10589955	MCF-7	breast:	n/a
30	chr8:10589905-10589955	ovcar-3	ovarian:	n/a
31	chr8:10589905-10589955	AG10803	skin:	n/a
32	chr8:10589905-10589955	Hela-S3	cervix:	n/a
33	chr8:10589905-10589955	Jurkat	blood:	n/a
34	chr8:10589905-10589955	MCF10A-Er-Src	breast:	n/a
35	chr8:10589905-10589955	SK-N-SH	brain:	n/a
36	chr8:10589905-10589955	HCT-116	colon:	n/a
37	chr8:10589905-10589955	SK-N-MC	brain:	n/a
38	chr8:10589905-10589955	H1-hESC	embryonic stem cell:	embryo
39	chr8:10589905-10589955	GM19239	blood:	n/a
40	chr8:10589905-10589955	U87	brain:	n/a
41	chr8:10589905-10589955	HEK293	kidney:	embryo
42	chr8:10589905-10589955	A549	lung:	n/a
43	chr8:10589905-10589955	HPAEpiC	pulmonary alveolar:	n/a
44	chr8:10589905-10589955	HCPEpiC	choroid plexus:	n/a
45	chr8:10589905-10589955	PANC-1	pancreas:	n/a
46	chr8:10589905-10589955	AG09309	skin:	n/a
47	chr8:10589905-10589955	IMR90	lung:	fetal
48	chr8:10589905-10589955	NHBE	bronchial:	n/a
49	chr8:10589905-10589955	HCM	heart:	n/a
50	chr8:10589905-10589955	K562	blood:	n/a

No data

Variant related genes	Relation type
SOX7	TF binding region
SOX7	CpG island

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10503409	0.90[CEU][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.91[TSI][hapmap]
rs10503410	0.85[CEU][hapmap]
rs11776368	1.00[CHD][hapmap]
rs11998382	0.81[CEU][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap]
rs12155811	0.90[CEU][hapmap]
rs12156345	1.00[CHD][hapmap]
rs12375394	0.90[CEU][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap]
rs12750	0.95[CEU][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap]
rs17718772	0.85[CEU][hapmap]
rs17720365	0.90[CEU][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap]
rs17721089	0.85[CEU][hapmap]
rs17774331	0.90[CEU][hapmap]
rs17774398	0.90[CEU][hapmap];0.80[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap]
rs17774627	0.90[CEU][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap]
rs17776404	0.85[CEU][hapmap]
rs17776427	0.90[CEU][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap]
rs17776497	0.89[CEU][hapmap]
rs17776622	0.90[CEU][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap]
rs17776946	0.90[CEU][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap]
rs2409654	1.00[CHD][hapmap]
rs2409655	1.00[CHD][hapmap]
rs4240671	1.00[CHD][hapmap]
rs4310166	1.00[CHD][hapmap]
rs4326350	1.00[CHD][hapmap]
rs4841458	1.00[CHD][hapmap]
rs60167323	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7002336	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7009920	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73200724	0.93[EUR][1000 genomes]
rs7817252	0.82[CEU][hapmap]
rs7825147	0.96[EUR][1000 genomes]
rs7827270	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs891558	0.95[CEU][hapmap]
rs891559	0.95[CEU][hapmap]
rs9650658	0.90[CEU][hapmap];1.00[CHD][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap]
rs9650659	0.90[CEU][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap]

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	nsv1022994	chr8:10190618-10660122	Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv539466	chr8:10190618-10660122	Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv917085	chr8:10237508-10828204	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1015932	chr8:10357101-10597856	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1021048	chr8:10504395-10591896	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
6	nsv527184	chr8:10530037-10589913	Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1034829	chr8:10537081-10591896	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv1022582	chr8:10571218-10636162	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv539468	chr8:10571218-10636162	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv1026802	chr8:10576444-10754489	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
11	nsv539469	chr8:10576444-10754489	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7838335	MFHAS1	cis	cerebellum	SCAN
rs7838335	DEFB136	cis	parietal	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10586600-10592600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
2	chr8:10587200-10592000	Bivalent Enhancer	Fetal Brain Male	brain
3	chr8:10587400-10590400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
4	chr8:10587400-10591200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr8:10587400-10592400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
6	chr8:10587400-10592400	Bivalent Enhancer	Placenta	Placenta
7	chr8:10588000-10592000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
8	chr8:10588000-10592400	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
9	chr8:10588200-10590000	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr8:10588200-10590800	Enhancers	Gastric	stomach
11	chr8:10588200-10591600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
12	chr8:10588400-10591600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
13	chr8:10588400-10592000	Enhancers	Lung	lung
14	chr8:10588400-10592200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
15	chr8:10588600-10590000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
16	chr8:10588600-10590600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr8:10588600-10591400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
18	chr8:10588600-10591600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr8:10588800-10590000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
20	chr8:10588800-10590000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
21	chr8:10588800-10590200	Enhancers	Liver	Liver
22	chr8:10588800-10590200	Weak transcription	HUVEC	blood vessel
23	chr8:10588800-10590400	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
24	chr8:10588800-10590600	Weak transcription	HMEC	breast
25	chr8:10588800-10592400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
26	chr8:10588800-10592400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr8:10589000-10590000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr8:10589000-10590200	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr8:10589000-10590200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr8:10589000-10590400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr8:10589000-10590600	Bivalent Enhancer	Fetal Muscle Leg	muscle
32	chr8:10589200-10590200	Bivalent Enhancer	Brain Cingulate Gyrus	brain
33	chr8:10589400-10590400	Bivalent Enhancer	Brain Anterior Caudate	brain
34	chr8:10589600-10590000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr8:10589600-10590000	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr8:10589600-10590000	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
37	chr8:10589600-10590200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr8:10589600-10590200	Bivalent Enhancer	Brain Substantia Nigra	brain
39	chr8:10589600-10590200	Bivalent Enhancer	Duodenum Mucosa	Duodenum
40	chr8:10589600-10590400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
41	chr8:10589600-10590400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
42	chr8:10589600-10590600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr8:10589600-10590600	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr8:10589600-10591200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr8:10589600-10592200	Bivalent Enhancer	Spleen	Spleen
46	chr8:10589600-10592600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
47	chr8:10589800-10590000	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr8:10589800-10590000	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr8:10589800-10590000	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
50	chr8:10589800-10590000	Bivalent Enhancer	Fetal Brain Female	brain

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