Variant report

Variant	rs7932354
Chromosome Location	chr11:46722221-46722222
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	TAF1	chr11:46721916-46722780	GM12878	blood:	n/a	n/a
2	USF1	chr11:46722019-46722609	A549	lung:	n/a	chr11:46722082-46722098
3	JUND	chr11:46721904-46722457	HepG2	liver:	n/a	n/a
4	ZNF384	chr11:46722047-46722654	K562	blood:	n/a	n/a
5	POLR2A	chr11:46721771-46722882	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr11:46721977-46722732	HepG2	liver:	n/a	n/a
7	POLR2A	chr11:46721758-46722776	HepG2	liver:	n/a	n/a
8	CHD2	chr11:46721894-46722685	K562	blood:	n/a	n/a
9	POLR2A	chr11:46721692-46722826	MCF10A-Er-Src	breast:	n/a	n/a
10	EBF1	chr11:46721937-46722515	GM12878	blood:	n/a	n/a
11	YY1	chr11:46721750-46722889	ECC-1	luminal epithelium:	n/a	chr11:46722241-46722250
12	USF1	chr11:46722142-46722410	HepG2	liver:	n/a	n/a
13	POLR2A	chr11:46721761-46722876	GM12878	blood:	n/a	n/a
14	FOXA1	chr11:46721881-46722446	T-47D	breast:	n/a	n/a
15	USF1	chr11:46722075-46722387	SK-N-SH_RA	brain:	n/a	chr11:46722082-46722098
16	HA-E2F1	chr11:46721655-46722831	MCF-7	breast:	n/a	chr11:46721919-46721928 chr11:46721913-46721930 chr11:46721920-46721927
17	RCOR1	chr11:46721994-46722618	K562	blood:	n/a	n/a
18	SRF	chr11:46722008-46722432	GM12878	blood:	n/a	chr11:46722260-46722270 chr11:46722237-46722250
19	MYC	chr11:46721859-46722640	K562	blood:	n/a	chr11:46722260-46722270
20	POLR2A	chr11:46721812-46722763	HepG2	liver:	n/a	n/a
21	EP300	chr11:46721723-46722778	ECC-1	luminal epithelium:	n/a	chr11:46722229-46722236 chr11:46722566-46722573
22	SIN3AK20	chr11:46721699-46722705	PFSK-1	brain:	n/a	n/a
23	MYC	chr11:46721939-46722550	K562	blood:	n/a	chr11:46722260-46722270
24	MAX	chr11:46721786-46722856	A549	lung:	n/a	chr11:46722260-46722270
25	STAT3	chr11:46722112-46722471	MCF10A-Er-Src	breast:	n/a	chr11:46722293-46722301 chr11:46722264-46722285
26	POLR2A	chr11:46721832-46722819	Gliobla	brain:	n/a	n/a
27	POLR2A	chr11:46721845-46722784	GM12891	blood:	n/a	n/a
28	USF1	chr11:46722099-46722568	K562	blood:	n/a	n/a
29	SIN3AK20	chr11:46721802-46722744	SK-N-SH	brain:	n/a	n/a
30	SIN3AK20	chr11:46721713-46722869	HCT-116	colon:	n/a	n/a
31	POLR2A	chr11:46721728-46723064	HL-60	blood:	n/a	n/a
32	FOXA1	chr11:46721875-46722415	HepG2	liver:	n/a	n/a
33	TAF1	chr11:46721860-46722467	HepG2	liver:	n/a	n/a
34	ELK4	chr11:46721884-46722685	HEK293	kidney:	n/a	chr11:46722266-46722277 chr11:46722565-46722574 chr11:46722226-46722237 chr11:46722204-46722215 chr11:46722228-46722237
35	RELA	chr11:46721828-46722870	GM15510	blood:	n/a	n/a
36	SRF	chr11:46721963-46722702	GM12878	blood:	n/a	chr11:46722260-46722270 chr11:46722237-46722250
37	SIN3AK20	chr11:46721716-46722508	PFSK-1	brain:	n/a	n/a
38	MAX	chr11:46721806-46722732	K562	blood:	n/a	chr11:46722260-46722270
39	FOSL2	chr11:46721666-46722773	A549	lung:	n/a	n/a
40	ATF2	chr11:46722076-46722780	GM12878	blood:	n/a	n/a
41	USF1	chr11:46722209-46722387	GM12878	blood:	n/a	n/a
42	TCF12	chr11:46721931-46722391	HepG2	liver:	n/a	n/a
43	TBL1XR1	chr11:46722160-46722860	K562	blood:	n/a	n/a
44	ZBTB7A	chr11:46721911-46722321	K562	blood:	n/a	n/a
45	POLR2A	chr11:46721770-46722859	U87	brain:	n/a	n/a
46	JUN	chr11:46721944-46722692	K562	blood:	n/a	n/a
47	SP1	chr11:46721817-46722817	A549	lung:	n/a	chr11:46722259-46722271 chr11:46722260-46722270 chr11:46722260-46722274 chr11:46722260-46722269 chr11:46722259-46722271 chr11:46722261-46722270 chr11:46722260-46722270 chr11:46721820-46721833
48	SPI1	chr11:46722017-46722467	HL-60	blood:	n/a	chr11:46722361-46722374 chr11:46722360-46722373
49	MYC	chr11:46721922-46722487	MCF-7	breast:	n/a	chr11:46722260-46722270
50	ZZZ3	chr11:46722184-46722701	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:46721576..46722295-chr17:56708607..56709333,2	Hela-S3	cervix:
2	chr11:46637616..46640198-chr11:46720757..46723705,2	MCF-7	breast:
3	chr11:46721749..46722600-chr20:37554852..37555545,2	Hela-S3	cervix:
4	chr11:46721624..46722687-chr17:7387250..7388279,3	Hela-S3	cervix:
5	chr11:46721125..46723767-chr11:46740816..46743369,3	K562	blood:
6	chr11:46637848..46640498-chr11:46721898..46723804,3	K562	blood:
7	chr11:46687606..46689855-chr11:46719361..46722282,2	K562	blood:
8	chr11:46614011..46615570-chr11:46721029..46722872,2	K562	blood:
9	chr11:46714752..46720031-chr11:46720626..46723177,8	MCF-7	breast:
10	chr11:46639444..46641700-chr11:46721393..46724232,2	K562	blood:
11	chr11:46721841..46722466-chr19:37019388..37020036,2	Hela-S3	cervix:
12	chr11:46721576..46722308-chr3:156892604..156893231,2	Hela-S3	cervix:
13	chr11:46722213..46727380-chr11:46743173..46747634,5	MCF-7	breast:
14	chr11:46693318..46696713-chr11:46720751..46722986,3	MCF-7	breast:
15	chr11:46722021..46722713-chr12:112846522..112847434,2	Hela-S3	cervix:

Variant related genes	Relation type
ARHGAP1	TF binding region
ZNF408	TF binding region
ENSG00000180210	Chromatin interaction
ENSG00000101447	Chromatin interaction
ENSG00000175220	Chromatin interaction
ENSG00000243176	Chromatin interaction
ENSG00000110497	Chromatin interaction
ENSG00000174282	Chromatin interaction
ENSG00000181222	Chromatin interaction
ENSG00000175224	Chromatin interaction
ENSG00000180423	Chromatin interaction
ENSG00000254004	Chromatin interaction
ENSG00000089009	Chromatin interaction
ENSG00000212195	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10769205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11606709	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12274785	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12361673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13448	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs2070852	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2282686	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2306029	0.90[JPT][hapmap];1.00[YRI][hapmap]
rs2306032	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3136505	0.83[EUR][1000 genomes]
rs4606447	0.94[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4752929	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57804402	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6485696	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs6485702	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9704782	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044225	chr11:46472580-46771102	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv541030	chr11:46472580-46771102	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

Variant related diseases (count:2)

Disease	PMID	Source
Bone mineral density (hip)	19801982	GWAS catalog
Bone mineral density	22504420	GWAS catalog

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:46720600-46722600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr11:46720800-46722800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:46720800-46723200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr11:46720800-46723200	Active TSS	Colon Smooth Muscle	Colon
5	chr11:46720800-46723200	Active TSS	NH-A	brain
6	chr11:46720800-46723400	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr11:46720800-46723600	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr11:46721000-46722600	Active TSS	Skeletal Muscle Male	skeletal muscle
9	chr11:46721000-46722800	Active TSS	Right Ventricle	heart
10	chr11:46721000-46722800	Active TSS	Stomach Smooth Muscle	stomach
11	chr11:46721000-46723000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr11:46721000-46723000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr11:46721000-46723000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr11:46721000-46723000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr11:46721000-46723000	Active TSS	Colonic Mucosa	Colon
16	chr11:46721000-46723000	Active TSS	Fetal Brain Female	brain
17	chr11:46721000-46723200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr11:46721000-46723200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr11:46721000-46723200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr11:46721000-46723200	Active TSS	Brain Cingulate Gyrus	brain
21	chr11:46721000-46723200	Active TSS	Duodenum Mucosa	Duodenum
22	chr11:46721000-46723200	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr11:46721000-46723200	Active TSS	Rectal Smooth Muscle	rectum
24	chr11:46721000-46723200	Active TSS	Hela-S3	cervix
25	chr11:46721000-46723200	Active TSS	HSMMtube	muscle
26	chr11:46721000-46723200	Active TSS	Osteobl	bone
27	chr11:46721000-46723400	Active TSS	Muscle Satellite Cultured Cells	--
28	chr11:46721000-46723400	Active TSS	NHDF-Ad	bronchial
29	chr11:46721000-46723400	Active TSS	NHLF	lung
30	chr11:46721000-46723600	Active TSS	HSMM	muscle
31	chr11:46721000-46723800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr11:46721200-46723000	Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr11:46721200-46723000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr11:46721200-46723000	Active TSS	Fetal Stomach	stomach
35	chr11:46721200-46723000	Active TSS	Psoas Muscle	Psoas
36	chr11:46721200-46723200	Active TSS	Aorta	Aorta
37	chr11:46721200-46723200	Active TSS	Fetal Intestine Small	intestine
38	chr11:46721200-46723200	Active TSS	Fetal Kidney	kidney
39	chr11:46721200-46723200	Active TSS	Fetal Lung	lung
40	chr11:46721200-46723200	Active TSS	Stomach Mucosa	stomach
41	chr11:46721200-46723200	Active TSS	A549	lung
42	chr11:46721200-46723400	Active TSS	H1 Cell Line	embryonic stem cell
43	chr11:46721200-46723400	Active TSS	H9 Cell Line	embryonic stem cell
44	chr11:46721200-46723400	Active TSS	HUES48 Cell Line	embryonic stem cell
45	chr11:46721200-46723400	Active TSS	iPS-15b Cell Line	embryonic stem cell
46	chr11:46721200-46723400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr11:46721200-46723400	Active TSS	GM12878-XiMat	blood
48	chr11:46721200-46723600	Active TSS	ES-I3 Cell Line	embryonic stem cell
49	chr11:46721200-46723600	Active TSS	HUES64 Cell Line	embryonic stem cell
50	chr11:46721200-46723600	Active TSS	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links