Variant report

Variant	rs10422283
Chromosome Location	chr19:42927521-42927522
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	JUND	chr19:42927258-42927608	H1-hESC	embryonic stem cell:	n/a	n/a
2	YY1	chr19:42927471-42927904	A549	lung:	n/a	chr19:42927651-42927665
3	SIX5	chr19:42927289-42927548	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr19:42926830-42928192	GM12878	blood:	n/a	n/a
5	CHD2	chr19:42927396-42928056	GM12878	blood:	n/a	n/a
6	POLR2A	chr19:42927474-42928729	H1-hESC	embryonic stem cell:	n/a	n/a
7	CHD2	chr19:42927511-42928641	H1-hESC	embryonic stem cell:	n/a	n/a
8	SP1	chr19:42926984-42928287	HCT-116	colon:	n/a	chr19:42927854-42927866 chr19:42927116-42927130 chr19:42928163-42928172 chr19:42927855-42927869 chr19:42927887-42927898 chr19:42928162-42928171 chr19:42928194-42928206 chr19:42928196-42928205 chr19:42928239-42928253 chr19:42927854-42927866 chr19:42927887-42927899 chr19:42927854-42927865 chr19:42928215-42928225 chr19:42927889-42927898 chr19:42927856-42927865 chr19:42927888-42927897 chr19:42927888-42927902 chr19:42927855-42927864 chr19:42927887-42927899
9	CHD1	chr19:42926733-42928070	GM12878	blood:	n/a	n/a
10	SP1	chr19:42927160-42928603	H1-hESC	embryonic stem cell:	n/a	chr19:42927854-42927866 chr19:42928323-42928332 chr19:42928163-42928172 chr19:42927855-42927869 chr19:42927887-42927898 chr19:42928162-42928171 chr19:42928194-42928206 chr19:42928196-42928205 chr19:42928239-42928253 chr19:42927854-42927866 chr19:42927887-42927899 chr19:42927854-42927865 chr19:42928321-42928333 chr19:42928215-42928225 chr19:42927889-42927898 chr19:42927856-42927865 chr19:42927888-42927897 chr19:42927888-42927902 chr19:42927855-42927864 chr19:42927887-42927899
11	SIN3AK20	chr19:42927515-42928070	A549	lung:	n/a	n/a
12	MAZ	chr19:42927073-42928214	GM12878	blood:	n/a	chr19:42928020-42928035 chr19:42928021-42928032 chr19:42928022-42928031 chr19:42928160-42928170 chr19:42928023-42928030 chr19:42927636-42927646 chr19:42928021-42928032
13	SIN3AK20	chr19:42927270-42927857	SK-N-SH	brain:	n/a	n/a
14	BACH1	chr19:42927187-42927770	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr19:42926774-42928253	GM12892	blood:	n/a	n/a
16	SIN3A	chr19:42926983-42928494	H1-hESC	embryonic stem cell:	n/a	chr19:42927986-42927999
17	SIN3A	chr19:42926858-42928026	GM12878	blood:	n/a	chr19:42927986-42927999
18	POLR2A	chr19:42926472-42928276	Raji	blood:	n/a	n/a
19	POLR2A	chr19:42927297-42928091	HCT-116	colon:	n/a	n/a
20	REST	chr19:42927430-42928191	A549	lung:	n/a	chr19:42927980-42927998 chr19:42927655-42927668 chr19:42927979-42927999 chr19:42927541-42927551
21	RCOR1	chr19:42927202-42928111	GM12878	blood:	n/a	n/a
22	USF1	chr19:42927301-42927557	SK-N-SH_RA	brain:	n/a	n/a
23	YY1	chr19:42927409-42928035	GM12892	blood:	n/a	chr19:42927651-42927665
24	E2F6	chr19:42927425-42928816	A549	lung:	n/a	chr19:42928201-42928211 chr19:42928458-42928469 chr19:42928162-42928171 chr19:42928385-42928394
25	POLR2A	chr19:42926811-42928161	GM12878	blood:	n/a	n/a
26	FOSL2	chr19:42927493-42928216	A549	lung:	n/a	n/a
27	MXI1	chr19:42927090-42928813	IMR90	lung:	n/a	n/a
28	REST	chr19:42926649-42928673	H1-neurons	neurons:	n/a	chr19:42927980-42927998 chr19:42927655-42927668 chr19:42927979-42927999 chr19:42927541-42927551
29	CHD1	chr19:42926653-42928296	IMR90	lung:	n/a	n/a
30	YY1	chr19:42927499-42927870	SK-N-SH_RA	brain:	n/a	chr19:42927651-42927665
31	ZEB1	chr19:42926851-42927757	GM12878	blood:	n/a	n/a
32	POLR2A	chr19:42926820-42928184	GM12891	blood:	n/a	n/a
33	TBP	chr19:42927330-42928539	H1-hESC	embryonic stem cell:	n/a	n/a
34	CHD1	chr19:42927123-42927699	H1-hESC	embryonic stem cell:	n/a	n/a
35	ELF1	chr19:42926690-42928210	GM12878	blood:	n/a	chr19:42927978-42927990
36	POLR2A	chr19:42926892-42928209	GM12878	blood:	n/a	n/a
37	SIX5	chr19:42927280-42927644	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr19:42926829-42928284	GM12878	blood:	n/a	n/a
39	ELF1	chr19:42926489-42928635	GM12878	blood:	n/a	chr19:42927978-42927990
40	POLR2A	chr19:42927499-42927900	U87	brain:	n/a	n/a
41	POLR2A	chr19:42926875-42928366	GM19193	blood:	n/a	n/a
42	MTA3	chr19:42926179-42928574	GM12878	blood:	n/a	n/a
43	SP1	chr19:42927207-42928512	H1-hESC	embryonic stem cell:	n/a	chr19:42927854-42927866 chr19:42928323-42928332 chr19:42928163-42928172 chr19:42927855-42927869 chr19:42927887-42927898 chr19:42928162-42928171 chr19:42928194-42928206 chr19:42928196-42928205 chr19:42928239-42928253 chr19:42927854-42927866 chr19:42927887-42927899 chr19:42927854-42927865 chr19:42928321-42928333 chr19:42928215-42928225 chr19:42927889-42927898 chr19:42927856-42927865 chr19:42927888-42927897 chr19:42927888-42927902 chr19:42927855-42927864 chr19:42927887-42927899
44	POLR2A	chr19:42926890-42928288	GM18951	blood:	n/a	n/a
45	POLR2A	chr19:42926940-42928261	GM15510	blood:	n/a	n/a
46	CEBPB	chr19:42927467-42928125	A549	lung:	n/a	n/a
47	NFATC1	chr19:42927202-42927789	GM12878	blood:	n/a	n/a
48	EP300	chr19:42927172-42927632	GM12878	blood:	n/a	n/a
49	PBX3	chr19:42927510-42928694	A549	lung:	n/a	n/a
50	POLR2A	chr19:42927324-42928039	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:42927142..42929606-chr19:42930289..42932952,2	MCF-7	breast:

Variant related genes	Relation type
LIPE-AS1	TF binding region
LIPE	TF binding region
ENSG00000079435	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10402677	0.82[CHB][hapmap]
rs10405891	0.80[AFR][1000 genomes]
rs10407576	0.85[CHB][hapmap]
rs10416915	0.80[AFR][1000 genomes]
rs10417560	0.81[AFR][1000 genomes]
rs10469285	0.82[CHB][hapmap]
rs10469286	0.85[CHB][hapmap]
rs11671846	0.82[CHB][hapmap]
rs11673645	0.82[CHB][hapmap]
rs16975750	0.81[AFR][1000 genomes]
rs16975890	0.85[CHB][hapmap]
rs2267631	0.85[CHB][hapmap]
rs34845087	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7248439	0.80[AFR][1000 genomes]
rs8102519	0.82[CHB][hapmap]
rs8103285	0.82[CHB][hapmap]
rs8107152	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv911782	chr19:42514712-42931004	Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	nsv526186	chr19:42676481-43203507	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
5	esv2422471	chr19:42733141-43669485	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
6	nsv911788	chr19:42887492-42930652	Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv911792	chr19:42901430-42929254	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv911793	chr19:42901430-42929502	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv911794	chr19:42901430-42930652	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv911795	chr19:42901430-42932699	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	nsv911798	chr19:42904653-42930652	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv911799	chr19:42905645-42930652	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
13	nsv911800	chr19:42906914-42930652	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv911801	chr19:42910416-42929502	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
15	nsv911802	chr19:42915110-42929254	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
16	nsv911804	chr19:42916841-42932699	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
17	nsv911806	chr19:42919405-42928397	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
18	nsv911807	chr19:42920555-42929254	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
19	nsv579633	chr19:42925636-42929254	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
20	nsv911808	chr19:42925636-42930652	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42925400-42928400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr19:42925800-42928400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
3	chr19:42926000-42928600	Flanking Active TSS	Primary B cells from cord blood	blood
4	chr19:42926200-42927600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr19:42926200-42927600	Flanking Active TSS	GM12878-XiMat	blood
6	chr19:42926200-42928400	Flanking Active TSS	Stomach Smooth Muscle	stomach
7	chr19:42926200-42929200	Flanking Active TSS	Adipose Nuclei	Adipose
8	chr19:42926400-42927600	Flanking Active TSS	Primary hematopoietic stem cells	blood
9	chr19:42926400-42927600	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
10	chr19:42926400-42928200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr19:42926400-42928200	Flanking Active TSS	HUVEC	blood vessel
12	chr19:42926400-42928400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
13	chr19:42926400-42928400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr19:42926600-42927600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
15	chr19:42926600-42927600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
16	chr19:42926600-42927600	Flanking Active TSS	Fetal Thymus	thymus
17	chr19:42926600-42927600	Flanking Active TSS	Spleen	Spleen
18	chr19:42926600-42928400	Flanking Active TSS	Colonic Mucosa	Colon
19	chr19:42926600-42928400	Active TSS	Fetal Kidney	kidney
20	chr19:42926600-42928600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
21	chr19:42926600-42928600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
22	chr19:42926600-42928600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
23	chr19:42926600-42928600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
24	chr19:42926600-42928600	Flanking Active TSS	HMEC	breast
25	chr19:42926800-42927600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr19:42926800-42927600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr19:42926800-42927600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr19:42926800-42927600	Flanking Active TSS	Lung	lung
29	chr19:42926800-42927600	Flanking Active TSS	NHLF	lung
30	chr19:42926800-42928400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
31	chr19:42926800-42928400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
32	chr19:42926800-42928400	Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr19:42926800-42928400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
34	chr19:42926800-42928600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
35	chr19:42926800-42928600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
36	chr19:42927000-42927600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
37	chr19:42927000-42927600	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr19:42927000-42927600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
39	chr19:42927000-42927600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr19:42927000-42927600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
41	chr19:42927000-42927600	Flanking Active TSS	A549	lung
42	chr19:42927000-42927600	Flanking Bivalent TSS/Enh	HepG2	liver
43	chr19:42927000-42927600	Flanking Active TSS	HSMM	muscle
44	chr19:42927000-42927800	Active TSS	Fetal Heart	heart
45	chr19:42927000-42928000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr19:42927000-42928000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr19:42927000-42928000	Active TSS	Fetal Brain Male	brain
48	chr19:42927000-42928200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr19:42927000-42928200	Active TSS	Gastric	stomach
50	chr19:42927000-42928400	Active TSS	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links