Variant report

Variant	rs6746622
Chromosome Location	chr2:101179122-101179123
allele	G/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	KAP1	chr2:101179033-101179649	U2OS	brain:	n/a	n/a
2	JUN	chr2:101178201-101180511	K562	blood:	n/a	chr2:101179689-101179698 chr2:101180362-101180373
3	CREB1	chr2:101179009-101179616	H1-hESC	embryonic stem cell:	n/a	n/a
4	EBF1	chr2:101179032-101179858	GM12878	blood:	n/a	n/a
5	SRF	chr2:101179078-101179420	HepG2	liver:	n/a	chr2:101179242-101179255 chr2:101179238-101179256 chr2:101179242-101179253 chr2:101179244-101179253 chr2:101179240-101179254 chr2:101179240-101179257
6	ELK1	chr2:101178916-101179947	GM12878	blood:	n/a	n/a
7	ATF2	chr2:101178954-101179955	GM12878	blood:	n/a	n/a
8	TBL1XR1	chr2:101179049-101179975	GM12878	blood:	n/a	n/a
9	POLR2A	chr2:101178503-101180157	GM19099	blood:	n/a	n/a
10	THAP1	chr2:101179026-101179959	K562	blood:	n/a	n/a
11	ELF1	chr2:101179016-101179912	K562	blood:	n/a	n/a
12	MAX	chr2:101178860-101180108	ECC-1	luminal epithelium:	n/a	n/a
13	CHD2	chr2:101179053-101180128	K562	blood:	n/a	n/a
14	TBP	chr2:101178911-101180027	K562	blood:	n/a	n/a
15	POLR2A	chr2:101178940-101180067	GM12891	blood:	n/a	n/a
16	E2F4	chr2:101179047-101179931	MCF10A-Er-Src	breast:	n/a	chr2:101179674-101179683
17	ATF2	chr2:101179000-101179484	H1-hESC	embryonic stem cell:	n/a	n/a
18	TCF3	chr2:101179009-101179302	GM12878	blood:	n/a	n/a
19	MEF2C	chr2:101178943-101179540	GM12878	blood:	n/a	chr2:101179114-101179128
20	GABPA	chr2:101179110-101179468	Hela-S3	cervix:	n/a	chr2:101179317-101179326 chr2:101179351-101179365
21	SP1	chr2:101179042-101179560	H1-hESC	embryonic stem cell:	n/a	chr2:101179408-101179417 chr2:101179215-101179225 chr2:101179473-101179487 chr2:101179407-101179416 chr2:101179210-101179219 chr2:101179478-101179487 chr2:101179406-101179418 chr2:101179214-101179226 chr2:101179214-101179226 chr2:101179406-101179418 chr2:101179476-101179488 chr2:101179199-101179213 chr2:101179476-101179488 chr2:101179477-101179486 chr2:101179215-101179224 chr2:101179426-101179440
22	JUND	chr2:101178726-101180250	K562	blood:	n/a	chr2:101179689-101179698
23	IRF4	chr2:101179024-101179366	GM12878	blood:	n/a	n/a
24	MAX	chr2:101179002-101180155	K562	blood:	n/a	n/a
25	YY1	chr2:101178979-101179516	A549	lung:	n/a	chr2:101179478-101179489 chr2:101179444-101179458 chr2:101179480-101179489
26	SIN3AK20	chr2:101179021-101180107	K562	blood:	n/a	n/a
27	SP1	chr2:101178940-101179678	H1-hESC	embryonic stem cell:	n/a	chr2:101179408-101179417 chr2:101179215-101179225 chr2:101179473-101179487 chr2:101179407-101179416 chr2:101179210-101179219 chr2:101179478-101179487 chr2:101179406-101179418 chr2:101179214-101179226 chr2:101179214-101179226 chr2:101179406-101179418 chr2:101179476-101179488 chr2:101179199-101179213 chr2:101179476-101179488 chr2:101179477-101179486 chr2:101179215-101179224 chr2:101179426-101179440
28	YY1	chr2:101179071-101179938	GM12892	blood:	n/a	chr2:101179478-101179489 chr2:101179444-101179458 chr2:101179480-101179489
29	MYC	chr2:101178929-101179550	MCF10A-Er-Src	breast:	n/a	n/a
30	GABPA	chr2:101178936-101179732	A549	lung:	n/a	chr2:101179670-101179684 chr2:101179317-101179326 chr2:101179673-101179682 chr2:101179351-101179365 chr2:101179673-101179687 chr2:101179673-101179684
31	BCL3	chr2:101179041-101179587	A549	lung:	n/a	chr2:101179478-101179487 chr2:101179473-101179486
32	POLR2A	chr2:101178971-101180080	MCF-7	breast:	n/a	n/a
33	STAT5A	chr2:101179073-101179631	K562	blood:	n/a	chr2:101179211-101179223
34	POLR2A	chr2:101178778-101180035	GM12878	blood:	n/a	n/a
35	MAZ	chr2:101178134-101180445	IMR90	lung:	n/a	chr2:101178474-101178489
36	CREB1	chr2:101178992-101179985	GM12878	blood:	n/a	n/a
37	CEBPD	chr2:101179074-101180071	HepG2	liver:	n/a	n/a
38	MEF2A	chr2:101178844-101179541	GM12878	blood:	n/a	chr2:101179114-101179128
39	MXI1	chr2:101178722-101180083	GM12878	blood:	n/a	n/a
40	TAF1	chr2:101178907-101180058	GM12878	blood:	n/a	n/a
41	CREB1	chr2:101179039-101179664	K562	blood:	n/a	n/a
42	POLR2A	chr2:101178781-101180144	HUVEC	blood vessel:	n/a	n/a
43	ZNF143	chr2:101179121-101179972	GM12878	blood:	n/a	chr2:101179483-101179493
44	SP1	chr2:101178876-101180002	A549	lung:	n/a	chr2:101179408-101179417 chr2:101179215-101179225 chr2:101179473-101179487 chr2:101179407-101179416 chr2:101179210-101179219 chr2:101179478-101179487 chr2:101179406-101179418 chr2:101179214-101179226 chr2:101179214-101179226 chr2:101179406-101179418 chr2:101179476-101179488 chr2:101179199-101179213 chr2:101179730-101179739 chr2:101179476-101179488 chr2:101179477-101179486 chr2:101179215-101179224 chr2:101179426-101179440
45	JUND	chr2:101179103-101180025	H1-hESC	embryonic stem cell:	n/a	chr2:101179689-101179698
46	POLR2A	chr2:101178821-101180127	H1-hESC	embryonic stem cell:	n/a	n/a
47	EP300	chr2:101178895-101180064	GM12878	blood:	n/a	chr2:101179732-101179748
48	POLR2A	chr2:101178930-101179996	A549	lung:	n/a	n/a
49	POLR2A	chr2:101178950-101180051	HepG2	liver:	n/a	n/a
50	POLR2A	chr2:101178766-101180075	GM18526	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:101179099-101179149	NHBE	bronchial:	n/a
2	chr2:101179099-101179149	AG10803	skin:	n/a
3	chr2:101179099-101179149	Hela-S3	cervix:	n/a
4	chr2:101179099-101179149	SK-N-SH_RA	brain:	n/a
5	chr2:101179099-101179149	NHDF-neo	bronchial:	n/a
6	chr2:101179099-101179149	HCT-116	colon:	n/a
7	chr2:101179099-101179149	GM12878	blood:	n/a
8	chr2:101179099-101179149	HEEpiC	esophagus:	n/a
9	chr2:101179099-101179149	CMK	blood:	n/a
10	chr2:101179099-101179149	ProgFib	skin:	n/a
11	chr2:101179099-101179149	K562	blood:	n/a
12	chr2:101179099-101179149	PrEC	prostate:	n/a
13	chr2:101179099-101179149	AG04450	lung:	fetal
14	chr2:101179099-101179149	A549	lung:	n/a
15	chr2:101179099-101179149	ECC-1	luminal epithelium:	n/a
16	chr2:101179099-101179149	SK-N-MC	brain:	n/a
17	chr2:101179099-101179149	SKMC	muscle:	n/a
18	chr2:101179099-101179149	HepG2	liver:	n/a
19	chr2:101179099-101179149	MCF-7	breast:	n/a
20	chr2:101179099-101179149	HMEC	breast:	n/a
21	chr2:101179099-101179149	HRCEpiC	kidney:	n/a
22	chr2:101179099-101179149	HEK293	kidney:	embryo
23	chr2:101179099-101179149	AG04449	skin:	fetal
24	chr2:101179099-101179149	Hepatocyte	liver:	n/a
25	chr2:101179099-101179149	NB4	blood:	n/a
26	chr2:101179099-101179149	HNPCEpiC	eye:	n/a
27	chr2:101179099-101179149	HCM	heart:	n/a
28	chr2:101179099-101179149	HCF	heart:	n/a
29	chr2:101179099-101179149	GM19239	blood:	n/a
30	chr2:101179099-101179149	GM12892	blood:	n/a
31	chr2:101179099-101179149	AoSMC	blood vessel:	n/a
32	chr2:101179099-101179149	HL-60	blood:	n/a
33	chr2:101179099-101179149	AG09319	gingival:	n/a
34	chr2:101179099-101179149	ovcar-3	ovarian:	n/a
35	chr2:101179099-101179149	NH-A	brain:	n/a
36	chr2:101179099-101179149	T-47D	breast:	n/a
37	chr2:101179099-101179149	HUVEC	blood vessel:	n/a
38	chr2:101179099-101179149	LNCaP	prostate:	n/a
39	chr2:101179099-101179149	U87	brain:	n/a
40	chr2:101179099-101179149	H1-hESC	embryonic stem cell:	embryo
41	chr2:101179099-101179149	HIPEpiC	eye:	n/a
42	chr2:101179099-101179149	MCF10A-Er-Src	breast:	n/a
43	chr2:101179099-101179149	PANC-1	pancreas:	n/a
44	chr2:101179099-101179149	PFSK-1	brain:	n/a
45	chr2:101179099-101179149	HCPEpiC	choroid plexus:	n/a
46	chr2:101179099-101179149	GM06990	blood:	n/a
47	chr2:101179099-101179149	HAEpiC	amniotic membrane:	n/a
48	chr2:101179099-101179149	SK-N-SH	brain:	n/a
49	chr2:101179099-101179149	Caco-2	colon:	n/a
50	chr2:101179099-101179149	BJ	skin:	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:101176864..101179772-chr2:101619065..101621695,2	MCF-7	breast:
2	chr2:101033038..101035627-chr2:101178228..101182939,5	K562	blood:
3	chr2:101177750..101180702-chr2:101616968..101620230,4	MCF-7	breast:
4	chr2:101178932..101179770-chr5:98264779..98265361,2	Hela-S3	cervix:
5	chr2:101177817..101179680-chr2:101183661..101186374,4	K562	blood:
6	chr2:101177993..101180966-chr2:101192692..101194735,2	K562	blood:
7	chr2:101177732..101180772-chr2:101616573..101620250,3	K562	blood:
8	chr2:101178645..101181337-chr2:101184679..101187696,4	MCF-7	breast:

Variant related genes	Relation type
PDCL3	TF binding region
PDCL3	CpG island
ENSG00000115539	Chromatin interaction
ENSG00000115526	Chromatin interaction
ENSG00000071082	Chromatin interaction
ENSG00000248489	Chromatin interaction
ENSG00000223947	Chromatin interaction
ENSG00000238328	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1052117	0.92[AMR][1000 genomes]
rs12469332	0.85[AMR][1000 genomes]
rs12622226	0.86[AMR][1000 genomes]
rs13418741	0.85[AMR][1000 genomes]
rs1533655	0.85[AMR][1000 genomes]
rs2309848	0.90[AMR][1000 genomes]
rs28560372	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28673254	0.84[AMR][1000 genomes]
rs28694778	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2971007	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61370232	0.93[AMR][1000 genomes]
rs62155213	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6739992	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6747613	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6748900	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6753993	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7557603	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7560366	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7594904	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7596475	0.94[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007777	chr2:100816913-101308914	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv535844	chr2:100816913-101308914	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv582531	chr2:100908508-101207639	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv916792	chr2:101021066-101525200	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv582532	chr2:101029002-101531943	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv834312	chr2:101044438-101238166	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:101178200-101179800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr2:101178400-101179200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr2:101178400-101180200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr2:101178400-101180200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:101178400-101180200	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr2:101178400-101180200	Active TSS	Fetal Brain Male	brain
7	chr2:101178400-101180200	Active TSS	Fetal Intestine Large	intestine
8	chr2:101178400-101180200	Active TSS	Fetal Stomach	stomach
9	chr2:101178400-101180400	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr2:101178400-101180400	Active TSS	Rectal Smooth Muscle	rectum
11	chr2:101178400-101180600	Active TSS	Fetal Brain Female	brain
12	chr2:101178400-101180600	Active TSS	Osteobl	bone
13	chr2:101178400-101180800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr2:101178400-101180800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr2:101178600-101179200	Flanking Active TSS	Primary B cells from cord blood	blood
16	chr2:101178600-101179200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
17	chr2:101178600-101179200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr2:101178600-101179400	Active TSS	Brain Germinal Matrix	brain
19	chr2:101178600-101180000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:101178600-101180200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr2:101178600-101180200	Active TSS	H1 Cell Line	embryonic stem cell
22	chr2:101178600-101180200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr2:101178600-101180200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr2:101178600-101180200	Active TSS	Colonic Mucosa	Colon
25	chr2:101178600-101180200	Active TSS	Fetal Intestine Small	intestine
26	chr2:101178600-101180200	Active TSS	Fetal Lung	lung
27	chr2:101178600-101180200	Active TSS	HMEC	breast
28	chr2:101178600-101180400	Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr2:101178600-101180400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr2:101178600-101180400	Active TSS	Fetal Kidney	kidney
31	chr2:101178600-101180400	Active TSS	Left Ventricle	heart
32	chr2:101178600-101180400	Active TSS	Right Atrium	heart
33	chr2:101178600-101180400	Active TSS	HSMMtube	muscle
34	chr2:101178600-101180400	Active TSS	NHEK	skin
35	chr2:101178600-101180600	Active TSS	H9 Cell Line	embryonic stem cell
36	chr2:101178600-101180600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr2:101178600-101180600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr2:101178600-101180600	Active TSS	HSMM	muscle
39	chr2:101178600-101180600	Active TSS	NHLF	lung
40	chr2:101178800-101179200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
41	chr2:101178800-101179400	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
42	chr2:101178800-101179400	Weak transcription	Fetal Heart	heart
43	chr2:101178800-101179400	Weak transcription	Gastric	stomach
44	chr2:101178800-101179400	Weak transcription	Stomach Mucosa	stomach
45	chr2:101178800-101179400	Weak transcription	Spleen	Spleen
46	chr2:101178800-101179800	Active TSS	Primary monocytes fromperipheralblood	blood
47	chr2:101178800-101179800	Active TSS	Primary T cells fromperipheralblood	blood
48	chr2:101178800-101179800	Active TSS	Primary hematopoietic stem cells	blood
49	chr2:101178800-101179800	Active TSS	Primary T helper cells fromperipheralblood	blood
50	chr2:101178800-101179800	Active TSS	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links