Variant report

Variant	rs11920635
Chromosome Location	chr3:113233917-113233918
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	chr3:113233728-113234300	K562	blood:	n/a	n/a
2	PML	chr3:113233718-113234251	MCF-7	breast:	n/a	chr3:113234136-113234144
3	BRCA1	chr3:113233047-113234197	Hela-S3	cervix:	n/a	n/a
4	FOXP2	chr3:113233580-113234172	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr3:113233500-113235394	MCF-7	breast:	n/a	n/a
6	TAF1	chr3:113233808-113234246	PFSK-1	brain:	n/a	n/a
7	NRF1	chr3:113233515-113234277	H1-hESC	embryonic stem cell:	n/a	chr3:113234082-113234096 chr3:113234085-113234096 chr3:113234085-113234094 chr3:113234084-113234095
8	ATF3	chr3:113233781-113234321	A549	lung:	n/a	n/a
9	TAL1	chr3:113233757-113233958	K562	blood:	n/a	n/a
10	POLR2A	chr3:113233658-113234437	GM12878	blood:	n/a	n/a
11	POLR2A	chr3:113233580-113234305	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr3:113233495-113234251	HL-60	blood:	n/a	n/a
13	FOXP2	chr3:113233821-113234136	PFSK-1	brain:	n/a	n/a
14	GABPA	chr3:113233352-113234508	MCF-7	breast:	n/a	chr3:113234082-113234096 chr3:113234085-113234096 chr3:113234085-113234094
15	PML	chr3:113233839-113234225	GM12878	blood:	n/a	chr3:113234136-113234144
16	NRF1	chr3:113233476-113234265	Hela-S3	cervix:	n/a	chr3:113234082-113234096 chr3:113234085-113234096 chr3:113234085-113234094 chr3:113234084-113234095
17	PAX5	chr3:113233805-113234171	GM12878	blood:	n/a	n/a
18	MAX	chr3:113233850-113234117	K562	blood:	n/a	chr3:113234051-113234060
19	POLR2A	chr3:113233575-113234351	K562	blood:	n/a	n/a
20	JUND	chr3:113233692-113234130	H1-hESC	embryonic stem cell:	n/a	n/a
21	YY1	chr3:113233878-113234238	A549	lung:	n/a	chr3:113234079-113234093
22	MAFK	chr3:113233345-113234152	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr3:113233686-113234294	GM12891	blood:	n/a	n/a
24	CREB1	chr3:113233797-113234253	ECC-1	luminal epithelium:	n/a	n/a
25	POLR2A	chr3:113233640-113234301	GM12891	blood:	n/a	n/a
26	NRF1	chr3:113233597-113234255	HepG2	liver:	n/a	chr3:113234082-113234096 chr3:113234085-113234096 chr3:113234085-113234094 chr3:113234084-113234095
27	POLR2A	chr3:113233462-113234358	GM12892	blood:	n/a	n/a
28	ELK1	chr3:113233794-113234199	Hela-S3	cervix:	n/a	n/a
29	YY1	chr3:113233624-113234147	GM12892	blood:	n/a	chr3:113234079-113234093
30	ELF1	chr3:113233594-113234208	A549	lung:	n/a	chr3:113233947-113233959
31	POLR2A	chr3:113233687-113234417	PANC-1	pancreas:	n/a	n/a
32	TBL1XR1	chr3:113233773-113234011	K562	blood:	n/a	n/a
33	GABPA	chr3:113233673-113234246	Hela-S3	cervix:	n/a	chr3:113234082-113234096 chr3:113234085-113234096 chr3:113234085-113234094
34	TCF12	chr3:113233493-113235250	A549	lung:	n/a	chr3:113234598-113234607
35	SP1	chr3:113233468-113234266	A549	lung:	n/a	chr3:113234046-113234055
36	MAZ	chr3:113233909-113234064	HepG2	liver:	n/a	chr3:113234051-113234060
37	POLR2A	chr3:113233762-113234206	A549	lung:	n/a	n/a
38	GATA3	chr3:113233892-113234227	T-47D	breast:	n/a	n/a
39	YY1	chr3:113233742-113234147	K562	blood:	n/a	chr3:113234079-113234093
40	POLR2A	chr3:113233484-113234392	Gliobla	brain:	n/a	n/a
41	HA-E2F1	chr3:113233325-113234602	MCF-7	breast:	n/a	chr3:113234086-113234095 chr3:113233801-113233811 chr3:113233764-113233774
42	GABPA	chr3:113233514-113234216	MCF-7	breast:	n/a	chr3:113234082-113234096 chr3:113234085-113234096 chr3:113234085-113234094
43	TAF1	chr3:113233545-113234206	Hela-S3	cervix:	n/a	n/a
44	SMARCB1	chr3:113233437-113234369	Hela-S3	cervix:	n/a	n/a
45	TAF1	chr3:113233805-113234207	SK-N-SH	brain:	n/a	n/a
46	MAX	chr3:113233537-113234095	HepG2	liver:	n/a	chr3:113234051-113234060
47	POLR2A	chr3:113233054-113235426	HepG2	liver:	n/a	n/a
48	POLR2A	chr3:113233521-113234224	H1-neurons	neurons:	n/a	n/a
49	POLR2A	chr3:113233450-113234332	K562	blood:	n/a	n/a
50	GABPA	chr3:113233538-113234256	SK-N-SH	brain:	n/a	chr3:113234082-113234096 chr3:113234085-113234096 chr3:113234085-113234094

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:113233880-113233930	SKMC	muscle:	n/a
2	chr3:113233880-113233930	MCF10A-Er-Src	breast:	n/a
3	chr3:113233880-113233930	LNCaP	prostate:	n/a
4	chr3:113233880-113233930	BE2_C	brain:	n/a
5	chr3:113233880-113233930	A549	lung:	n/a
6	chr3:113233880-113233930	NT2-D1	testis:	n/a
7	chr3:113233880-113233930	HRPEpiC	eye:	n/a
8	chr3:113233880-113233930	NHBE	bronchial:	n/a
9	chr3:113233880-113233930	BJ	skin:	n/a
10	chr3:113233880-113233930	AoSMC	blood vessel:	n/a
11	chr3:113233880-113233930	HUVEC	blood vessel:	n/a
12	chr3:113233880-113233930	RPTEC	kidney:	n/a
13	chr3:113233880-113233930	HL-60	blood:	n/a
14	chr3:113233880-113233930	HEK293	kidney:	embryo
15	chr3:113233880-113233930	AG04449	skin:	fetal
16	chr3:113233880-113233930	GM19239	blood:	n/a
17	chr3:113233880-113233930	PANC-1	pancreas:	n/a
18	chr3:113233880-113233930	AG10803	skin:	n/a
19	chr3:113233880-113233930	GM12878	blood:	n/a
20	chr3:113233880-113233930	NH-A	brain:	n/a
21	chr3:113233880-113233930	AG09319	gingival:	n/a
22	chr3:113233880-113233930	HCT-116	colon:	n/a
23	chr3:113233880-113233930	AG09309	skin:	n/a
24	chr3:113233880-113233930	HAEpiC	amniotic membrane:	n/a
25	chr3:113233880-113233930	Caco-2	colon:	n/a
26	chr3:113233880-113233930	PFSK-1	brain:	n/a
27	chr3:113233880-113233930	AG04450	lung:	fetal
28	chr3:113233880-113233930	HIPEpiC	eye:	n/a
29	chr3:113233880-113233930	HCM	heart:	n/a
30	chr3:113233880-113233930	HMEC	breast:	n/a
31	chr3:113233880-113233930	SK-N-SH	brain:	n/a
32	chr3:113233880-113233930	ovcar-3	ovarian:	n/a
33	chr3:113233880-113233930	HPAEpiC	pulmonary alveolar:	n/a
34	chr3:113233880-113233930	HNPCEpiC	eye:	n/a
35	chr3:113233880-113233930	GM06990	blood:	n/a
36	chr3:113233880-113233930	T-47D	breast:	n/a
37	chr3:113233880-113233930	H1-hESC	embryonic stem cell:	embryo
38	chr3:113233880-113233930	HEEpiC	esophagus:	n/a
39	chr3:113233880-113233930	HCPEpiC	choroid plexus:	n/a
40	chr3:113233880-113233930	HepG2	liver:	n/a
41	chr3:113233880-113233930	IMR90	lung:	fetal
42	chr3:113233880-113233930	HRCEpiC	kidney:	n/a
43	chr3:113233880-113233930	ProgFib	skin:	n/a
44	chr3:113233880-113233930	ECC-1	luminal epithelium:	n/a
45	chr3:113233880-113233930	HCF	heart:	n/a
46	chr3:113233880-113233930	SK-N-SH_RA	brain:	n/a
47	chr3:113233880-113233930	GM12892	blood:	n/a
48	chr3:113233880-113233930	Hepatocyte	liver:	n/a
49	chr3:113233880-113233930	NB4	blood:	n/a
50	chr3:113233880-113233930	Hela-S3	cervix:	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:113229615..113239929-chr3:113247196..113257849,45	MCF-7	breast:
2	chr3:112279637..112281423-chr3:113232414..113235211,2	K562	blood:
3	chr3:113232695..113235446-chr3:113249011..113251267,3	K562	blood:
4	chr3:112709917..112711539-chr3:113232036..113234156,2	K562	blood:
5	chr3:113233753..113235613-chr3:113463995..113467002,3	MCF-7	breast:
6	chr3:113232788..113235774-chr3:113464780..113467765,2	MCF-7	breast:

Variant related genes	Relation type
SPICE1	TF binding region
SPICE1	CpG island
ENSG00000114573	Chromatin interaction
ENSG00000272844	Chromatin interaction
ENSG00000163607	Chromatin interaction
ENSG00000242659	Chromatin interaction
ENSG00000072858	Chromatin interaction
ENSG00000144848	Chromatin interaction
ENSG00000121579	Chromatin interaction
ENSG00000138459	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11919330	0.87[YRI][hapmap]
rs11922708	1.00[AMR][1000 genomes]
rs11924109	0.88[AFR][1000 genomes]
rs16860995	1.00[AMR][1000 genomes]
rs16861014	1.00[ASW][hapmap];0.92[LWK][hapmap];1.00[MKK][hapmap];0.87[YRI][hapmap]
rs16861025	0.87[YRI][hapmap]
rs16861032	0.87[YRI][hapmap]
rs16861045	1.00[ASW][hapmap];0.92[LWK][hapmap];1.00[MKK][hapmap];0.87[YRI][hapmap]
rs16861077	0.87[YRI][hapmap]
rs16861115	0.87[YRI][hapmap]
rs2306068	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs2306070	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs61065093	0.88[AFR][1000 genomes]
rs6783691	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv1004000	chr3:113116778-113513899	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv877349	chr3:113208224-113323787	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
4	nsv877350	chr3:113208224-113332235	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113232400-113235200	Active TSS	A549	lung
2	chr3:113232600-113234000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr3:113232600-113234400	Active TSS	HMEC	breast
4	chr3:113232600-113234600	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr3:113232600-113234600	Active TSS	GM12878-XiMat	blood
6	chr3:113232600-113234600	Active TSS	K562	blood
7	chr3:113232600-113234600	Active TSS	Osteobl	bone
8	chr3:113232600-113234800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:113232600-113234800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:113232600-113234800	Active TSS	Right Ventricle	heart
11	chr3:113232600-113235000	Active TSS	Thymus	Thymus
12	chr3:113232600-113235000	Active TSS	NHLF	lung
13	chr3:113232800-113234000	Flanking Active TSS	Primary B cells from cord blood	blood
14	chr3:113232800-113234600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr3:113232800-113234600	Active TSS	Brain Germinal Matrix	brain
16	chr3:113232800-113234600	Active TSS	Fetal Stomach	stomach
17	chr3:113232800-113234800	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr3:113232800-113234800	Active TSS	H1 Cell Line	embryonic stem cell
19	chr3:113232800-113235000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:113232800-113235200	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr3:113233000-113234000	ZNF genes & repeats	Fetal Brain Male	brain
22	chr3:113233000-113234000	Bivalent/Poised TSS	HepG2	liver
23	chr3:113233000-113234400	Active TSS	Fetal Thymus	thymus
24	chr3:113233000-113234600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:113233000-113234600	Active TSS	Muscle Satellite Cultured Cells	--
26	chr3:113233000-113234600	Active TSS	Fetal Muscle Trunk	muscle
27	chr3:113233000-113234600	Active TSS	Placenta Amnion	Placenta Amnion
28	chr3:113233000-113234600	Active TSS	Stomach Mucosa	stomach
29	chr3:113233000-113234600	Active TSS	Hela-S3	cervix
30	chr3:113233000-113234600	Active TSS	HSMMtube	muscle
31	chr3:113233000-113234800	Active TSS	H9 Cell Line	embryonic stem cell
32	chr3:113233000-113234800	Active TSS	HUES6 Cell Line	embryonic stem cell
33	chr3:113233000-113234800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr3:113233000-113234800	Active TSS	Fetal Intestine Large	intestine
35	chr3:113233000-113234800	Active TSS	Fetal Intestine Small	intestine
36	chr3:113233000-113234800	Active TSS	Stomach Smooth Muscle	stomach
37	chr3:113233000-113234800	Active TSS	HSMM	muscle
38	chr3:113233000-113234800	Active TSS	NHDF-Ad	bronchial
39	chr3:113233000-113235000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:113233000-113235000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr3:113233000-113235000	Active TSS	Right Atrium	heart
42	chr3:113233000-113235200	Active TSS	Rectal Mucosa Donor 29	rectum
43	chr3:113233000-113235400	Active TSS	Psoas Muscle	Psoas
44	chr3:113233200-113234000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
45	chr3:113233200-113234400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr3:113233200-113234400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr3:113233200-113234400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:113233200-113234400	Active TSS	Gastric	stomach
49	chr3:113233200-113234600	Active TSS	iPS-15b Cell Line	embryonic stem cell
50	chr3:113233200-113234600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links