Variant report

Variant	rs3755817
Chromosome Location	chr3:53879372-53879373
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	POLR2A	chr3:53879209-53879389	Hela-S3	cervix:	n/a	n/a
2	EGR1	chr3:53879200-53880009	HCT-116	colon:	n/a	chr3:53879642-53879655 chr3:53879645-53879654 chr3:53879644-53879666 chr3:53879648-53879662 chr3:53879648-53879661 chr3:53879643-53879654 chr3:53879649-53879660 chr3:53879642-53879656 chr3:53879642-53879655 chr3:53879649-53879663 chr3:53879651-53879660 chr3:53879642-53879655
3	MAX	chr3:53879200-53880964	HCT-116	colon:	n/a	n/a
4	ZNF143	chr3:53879341-53879905	Hela-S3	cervix:	n/a	n/a
5	MBD4	chr3:53878488-53879580	HepG2	liver:	n/a	n/a
6	HEY1	chr3:53876036-53880070	HepG2	liver:	n/a	n/a
7	HEY1	chr3:53876129-53880020	HepG2	liver:	n/a	n/a
8	POLR2A	chr3:53877216-53879627	HepG2	liver:	n/a	n/a
9	POLR2A	chr3:53879199-53880967	GM18526	blood:	n/a	n/a
10	MAX	chr3:53879218-53881061	HCT-116	colon:	n/a	n/a
11	POLR2A	chr3:53876086-53880024	HepG2	liver:	n/a	n/a
12	POLR2A	chr3:53876459-53880951	HepG2	liver:	n/a	n/a
13	ZNF143	chr3:53879276-53879885	GM12878	blood:	n/a	n/a
14	POLR2A	chr3:53879116-53881395	GM19099	blood:	n/a	n/a
15	POLR2A	chr3:53875240-53880984	HepG2	liver:	n/a	n/a
16	EGR1	chr3:53879231-53880057	HCT-116	colon:	n/a	chr3:53879642-53879655 chr3:53879645-53879654 chr3:53879644-53879666 chr3:53879648-53879662 chr3:53879648-53879661 chr3:53879643-53879654 chr3:53879649-53879660 chr3:53879642-53879656 chr3:53879642-53879655 chr3:53879649-53879663 chr3:53879651-53879660 chr3:53879642-53879655
17	POLR2A	chr3:53877904-53881035	GM19193	blood:	n/a	n/a
18	POLR2A	chr3:53877360-53880992	GM18951	blood:	n/a	n/a
19	TAF1	chr3:53878057-53879395	HepG2	liver:	n/a	n/a
20	EGR1	chr3:53879359-53879874	ECC-1	luminal epithelium:	n/a	chr3:53879642-53879655 chr3:53879645-53879654 chr3:53879644-53879666 chr3:53879648-53879662 chr3:53879648-53879661 chr3:53879643-53879654 chr3:53879649-53879660 chr3:53879642-53879656 chr3:53879642-53879655 chr3:53879649-53879663 chr3:53879651-53879660 chr3:53879642-53879655
21	POLR2A	chr3:53879351-53880858	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr3:53876293-53881852	HepG2	liver:	n/a	n/a
23	POLR2A	chr3:53876116-53879632	HepG2	liver:	n/a	n/a
24	RCOR1	chr3:53879328-53879981	Hela-S3	cervix:	n/a	n/a
25	ZNF143	chr3:53879294-53879917	H1-hESC	embryonic stem cell:	n/a	n/a
26	CTCF	chr3:53879306-53880134	A549	lung:	n/a	n/a
27	RCOR1	chr3:53879305-53879745	GM12878	blood:	n/a	n/a
28	MAZ	chr3:53879367-53879432	HepG2	liver:	n/a	n/a
29	MYBL2	chr3:53878313-53879708	HepG2	liver:	n/a	n/a
30	TBP	chr3:53876673-53879496	HepG2	liver:	n/a	n/a
31	POLR2A	chr3:53878844-53879451	HepG2	liver:	n/a	n/a
32	POLR2A	chr3:53876680-53880844	GM12891	blood:	n/a	n/a
33	RFX5	chr3:53878396-53879539	HepG2	liver:	n/a	n/a
34	SMARCB1	chr3:53879250-53880928	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr3:53876430-53879414	HepG2	liver:	n/a	n/a
36	YY1	chr3:53878407-53879407	HepG2	liver:	n/a	n/a
37	RELA	chr3:53879345-53879981	GM19099	blood:	n/a	n/a
38	MAX	chr3:53876250-53881108	HepG2	liver:	n/a	chr3:53878578-53878587
39	SMC3	chr3:53879362-53879635	HepG2	liver:	n/a	n/a
40	POLR2A	chr3:53876647-53879870	HepG2	liver:	n/a	n/a
41	WRNIP1	chr3:53879100-53879945	GM12878	blood:	n/a	n/a
42	POLR2A	chr3:53879211-53880998	GM12878	blood:	n/a	n/a
43	RCOR1	chr3:53878462-53879692	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:53288526..53291244-chr3:53879304..53881119,2	MCF-7	breast:

Variant related genes	Relation type
CHDH	TF binding region
IL17RB	TF binding region
ENSG00000163931	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1025690	0.86[EUR][1000 genomes]
rs17641133	0.94[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2118421	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2232330	0.91[ASN][1000 genomes]
rs2232333	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2276839	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs2289205	0.90[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4546140	0.83[EUR][1000 genomes]
rs45560831	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs45616236	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55974100	0.89[EUR][1000 genomes]
rs56052250	0.89[EUR][1000 genomes]
rs62250937	0.85[ASN][1000 genomes]
rs62250939	0.85[ASN][1000 genomes]
rs920253	1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][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	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv876803	chr3:53822893-53889849	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv518466	chr3:53832903-53882663	Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv521181	chr3:53833509-53881471	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv876804	chr3:53833509-53934171	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	nsv1010575	chr3:53846741-53934781	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv1006990	chr3:53849510-54285212	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
10	nsv997771	chr3:53852695-53926635	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
11	nsv1002141	chr3:53858541-53934781	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
12	nsv876805	chr3:53865731-53883722	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3755817	IL17RB	cis	cerebellum	SCAN
rs3755817	SEMA3G	cis	parietal	SCAN
rs3755817	CACNA1D	cis	cerebellum	SCAN
rs3755817	ACTR8	cis	parietal	SCAN
rs3755817	ACTR8	cis	cerebellum	SCAN
rs3755817	IL17RB	Cis_1M	lymphoblastoid	RTeQTL
rs3755817	CHDH	cis	Nerve Tibial	GTEx

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53846600-53879800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:53854000-53879400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:53865600-53879800	Weak transcription	Aorta	Aorta
4	chr3:53869600-53879600	Weak transcription	Right Atrium	heart
5	chr3:53870800-53879600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:53875200-53879400	Enhancers	H1 Cell Line	embryonic stem cell
7	chr3:53876200-53879600	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr3:53876400-53879400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:53876600-53879600	Enhancers	Lung	lung
10	chr3:53877000-53879400	Weak transcription	Fetal Kidney	kidney
11	chr3:53877400-53879400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr3:53877400-53879800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
13	chr3:53877600-53879400	Weak transcription	Right Ventricle	heart
14	chr3:53877600-53879600	Weak transcription	Spleen	Spleen
15	chr3:53877600-53879800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr3:53878000-53879400	Flanking Active TSS	Liver	Liver
17	chr3:53878000-53879400	Enhancers	Small Intestine	intestine
18	chr3:53878000-53879600	Flanking Active TSS	Duodenum Mucosa	Duodenum
19	chr3:53878000-53879800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
20	chr3:53878000-53880200	Active TSS	Stomach Smooth Muscle	stomach
21	chr3:53878200-53879400	Weak transcription	Esophagus	oesophagus
22	chr3:53878400-53879600	Flanking Active TSS	Pancreas	Pancrea
23	chr3:53878600-53879400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr3:53878600-53879600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
25	chr3:53878600-53879800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
26	chr3:53878600-53879800	Flanking Active TSS	Fetal Intestine Large	intestine
27	chr3:53878600-53880000	Flanking Active TSS	GM12878-XiMat	blood
28	chr3:53878800-53879400	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
29	chr3:53878800-53879400	Active TSS	Skeletal Muscle Male	skeletal muscle
30	chr3:53878800-53879400	Flanking Bivalent TSS/Enh	HepG2	liver
31	chr3:53878800-53879600	Flanking Active TSS	Brain Hippocampus Middle	brain
32	chr3:53878800-53879800	Flanking Active TSS	Brain Cingulate Gyrus	brain
33	chr3:53879000-53879400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:53879000-53879400	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
35	chr3:53879000-53879400	Enhancers	Stomach Mucosa	stomach
36	chr3:53879000-53879400	Enhancers	A549	lung
37	chr3:53879000-53879600	Flanking Active TSS	Brain Substantia Nigra	brain
38	chr3:53879000-53879600	Bivalent Enhancer	Fetal Brain Female	brain
39	chr3:53879000-53879600	Flanking Active TSS	Hela-S3	cervix
40	chr3:53879000-53879600	Weak transcription	HMEC	breast
41	chr3:53879000-53879800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr3:53879000-53879800	Flanking Active TSS	Fetal Intestine Small	intestine
43	chr3:53879200-53879400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
44	chr3:53879200-53879400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
45	chr3:53879200-53879400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
46	chr3:53879200-53879400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
47	chr3:53879200-53879400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr3:53879200-53879400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:53879200-53879400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr3:53879200-53879400	Bivalent Enhancer	Brain Germinal Matrix	brain

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