Variant report

Variant	rs4948106
Chromosome Location	chr7:56167595-56167596
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:76)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:76 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:56165849-56169236	PANC-1	pancreas:	n/a	n/a
2	CTCF	chr7:56167500-56167650	HepG2	liver:	n/a	n/a
3	POLR2A	chr7:56167370-56168976	SK-N-SH	brain:	n/a	n/a
4	CHD2	chr7:56167560-56167752	K562	blood:	n/a	n/a
5	POLR2A	chr7:56166076-56169320	GM12878	blood:	n/a	n/a
6	POLR2A	chr7:56167433-56167865	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr7:56167048-56169396	K562	blood:	n/a	n/a
8	PML	chr7:56167477-56168142	K562	blood:	n/a	n/a
9	POLR2A	chr7:56167023-56169284	HepG2	liver:	n/a	n/a
10	CTCF	chr7:56167460-56167610	GM12878	blood:	n/a	n/a
11	POLR2A	chr7:56167427-56169013	U87	brain:	n/a	n/a
12	POLR2A	chr7:56167427-56167794	GM12878	blood:	n/a	n/a
13	POLR2A	chr7:56166044-56170051	K562	blood:	n/a	n/a
14	POLR2A	chr7:56166771-56169276	A549	lung:	n/a	n/a
15	CTCF	chr7:56167520-56167670	GM12873	blood:	n/a	n/a
16	CTCF	chr7:56167460-56167610	GM12865	blood:	n/a	n/a
17	CTCF	chr7:56167460-56167610	GM12864	blood:	n/a	n/a
18	POLR2A	chr7:56165178-56175093	K562	blood:	n/a	n/a
19	POLR2A	chr7:56166020-56169262	K562	blood:	n/a	n/a
20	POLR2A	chr7:56167059-56169406	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr7:56167466-56168284	U87	brain:	n/a	n/a
22	POLR2A	chr7:56167072-56167636	PANC-1	pancreas:	n/a	n/a
23	POLR2A	chr7:56166185-56168586	GM12891	blood:	n/a	n/a
24	PML	chr7:56167358-56167957	K562	blood:	n/a	n/a
25	POLR2A	chr7:56167230-56169162	K562	blood:	n/a	n/a
26	HEY1	chr7:56167370-56167960	K562	blood:	n/a	n/a
27	POLR2A	chr7:56167338-56168870	Hela-S3	cervix:	n/a	n/a
28	RCOR1	chr7:56167456-56167617	HepG2	liver:	n/a	n/a
29	POLR2A	chr7:56166883-56169354	K562	blood:	n/a	n/a
30	POLR2A	chr7:56167385-56167798	SK-N-SH	brain:	n/a	n/a
31	POLR2A	chr7:56167379-56167666	HCT-116	colon:	n/a	n/a
32	POLR2A	chr7:56166012-56168947	PFSK-1	brain:	n/a	n/a
33	POLR2A	chr7:56167019-56168645	MCF10A-Er-Src	breast:	n/a	n/a
34	POLR2A	chr7:56166562-56169354	K562	blood:	n/a	n/a
35	CTCF	chr7:56167460-56167610	GM12873	blood:	n/a	n/a
36	POLR2A	chr7:56167389-56169442	SK-N-MC	brain:	n/a	n/a
37	POLR2A	chr7:56165333-56169250	GM12878	blood:	n/a	n/a
38	POLR2A	chr7:56167451-56167602	Hela-S3	cervix:	n/a	n/a
39	CHD2	chr7:56167525-56167655	HepG2	liver:	n/a	n/a
40	CTCF	chr7:56167580-56167730	HBMEC	blood vessel:	n/a	n/a
41	POLR2A	chr7:56167033-56168683	HL-60	blood:	n/a	n/a
42	POLR2A	chr7:56165965-56169413	GM12892	blood:	n/a	n/a
43	POLR2A	chr7:56166941-56168156	PFSK-1	brain:	n/a	n/a
44	POLR2A	chr7:56166059-56169202	K562	blood:	n/a	n/a
45	POLR2A	chr7:56166128-56169485	GM12878	blood:	n/a	n/a
46	POLR2A	chr7:56167498-56167709	U87	brain:	n/a	n/a
47	POLR2A	chr7:56166001-56169490	K562	blood:	n/a	n/a
48	POLR2A	chr7:56165277-56169953	GM12891	blood:	n/a	n/a
49	CTCF	chr7:56167540-56167690	HMF	breast:	n/a	n/a
50	POLR2A	chr7:56167337-56168534	HepG2	liver:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:56166954..56169953-chr7:56173700..56175335,2	MCF-7	breast:
2	chr7:56158331..56162402-chr7:56164304..56169225,5	K562	blood:
3	chr7:56128361..56131760-chr7:56167519..56170434,3	K562	blood:
4	chr7:56165783..56167904-chr7:56180096..56183560,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000238673	TF binding region
ENSG00000106153	Chromatin interaction
ENSG00000129103	Chromatin interaction
ENSG00000146731	Chromatin interaction
ENSG00000164776	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10255049	0.86[ASN][1000 genomes]
rs10258800	0.85[AMR][1000 genomes]
rs11238394	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11773374	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11773453	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12537943	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13234899	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13242830	0.85[AMR][1000 genomes]
rs13244654	0.89[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.84[LWK][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1894832	0.85[CEU][hapmap];0.85[AMR][1000 genomes]
rs2002651	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2016482	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2016724	0.88[CEU][hapmap];0.82[AMR][1000 genomes]
rs2242508	0.81[CHB][hapmap];0.83[CHD][hapmap];0.81[LWK][hapmap]
rs2331180	0.84[CEU][hapmap];0.85[AMR][1000 genomes]
rs2538047	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2908543	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2908544	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2908545	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2908550	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4275190	0.81[CHB][hapmap]
rs4947536	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6593297	0.81[CHB][hapmap]
rs6945795	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7782243	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7783339	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7793921	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7799471	0.85[AMR][1000 genomes]
rs7801169	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs816408	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs816409	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs816411	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs860118	0.85[CEU][hapmap]
rs933466	0.85[CEU][hapmap];0.91[GIH][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes]
rs9767946	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829874	chr7:55382925-56369816	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv995105	chr7:55606107-56174888	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	esv12412	chr7:55619800-56385412	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv949574	chr7:55705566-56544711	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	esv3446617	chr7:55745934-56485903	Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
6	nsv529162	chr7:55800753-56174888	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	esv2761334	chr7:55823581-56424739	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
8	nsv1018806	chr7:55844931-56383936	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
9	nsv538860	chr7:55844931-56383936	Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
10	nsv498114	chr7:55872850-56174888	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
11	nsv1034712	chr7:56146885-56605592	Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
12	nsv538861	chr7:56146885-56605592	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4948106	SUMF2	cis	parietal	SCAN
rs4948106	SUMF2	cis	cerebellum	SCAN
rs4948106	CHCHD2	cis	parietal	SCAN
rs4948106	CHCHD2	cis	cerebellum	SCAN
rs4948106	GBAS	cis	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56134000-56167800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr7:56134200-56167600	Weak transcription	Small Intestine	intestine
3	chr7:56138800-56167600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr7:56142000-56168000	Weak transcription	GM12878-XiMat	blood
5	chr7:56142200-56167800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr7:56146000-56167800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr7:56147400-56169800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr7:56149800-56167600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr7:56149800-56168000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr7:56155600-56167600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr7:56157800-56167600	Weak transcription	K562	blood
12	chr7:56158200-56173200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr7:56159600-56168200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr7:56160600-56167600	Weak transcription	Psoas Muscle	Psoas
15	chr7:56160800-56170400	Weak transcription	Fetal Brain Male	brain
16	chr7:56161000-56167600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr7:56161000-56167600	Weak transcription	HSMM	muscle
18	chr7:56161000-56173000	Weak transcription	Fetal Heart	heart
19	chr7:56161200-56167600	Weak transcription	Colonic Mucosa	Colon
20	chr7:56161200-56167600	Weak transcription	Esophagus	oesophagus
21	chr7:56161200-56167600	Weak transcription	Left Ventricle	heart
22	chr7:56161200-56167600	Weak transcription	Right Ventricle	heart
23	chr7:56161200-56167600	Weak transcription	Spleen	Spleen
24	chr7:56161200-56167600	Weak transcription	HepG2	liver
25	chr7:56161200-56167600	Weak transcription	HUVEC	blood vessel
26	chr7:56161200-56167800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr7:56161200-56169600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr7:56161200-56173000	Weak transcription	Right Atrium	heart
29	chr7:56161400-56167600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr7:56164000-56172800	Strong transcription	Fetal Stomach	stomach
31	chr7:56164200-56171600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr7:56164200-56172000	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr7:56164200-56172600	Strong transcription	Fetal Intestine Small	intestine
34	chr7:56165000-56172200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr7:56165200-56172000	Strong transcription	Fetal Brain Female	brain
36	chr7:56165200-56172800	Strong transcription	Thymus	Thymus
37	chr7:56165400-56171400	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr7:56165400-56172000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr7:56165400-56172200	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr7:56165400-56172200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr7:56165400-56172400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr7:56165600-56167600	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr7:56165800-56167600	Weak transcription	Pancreas	Pancrea
44	chr7:56166000-56171800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr7:56166200-56172200	Strong transcription	Fetal Intestine Large	intestine
46	chr7:56166200-56172200	Strong transcription	Fetal Thymus	thymus
47	chr7:56166200-56172600	Strong transcription	Fetal Muscle Leg	muscle
48	chr7:56166400-56167600	Weak transcription	NHDF-Ad	bronchial
49	chr7:56166400-56170400	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr7:56166400-56172200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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