Variant report

Variant	rs6976303
Chromosome Location	chr7:39662925-39662926
allele	A/G
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	STAT5A	chr7:39662775-39663478	GM12878	blood:	n/a	chr7:39662834-39662846 chr7:39663116-39663123
2	POLR2A	chr7:39662642-39663379	HepG2	liver:	n/a	n/a
3	POLR2A	chr7:39662849-39663607	A549	lung:	n/a	n/a
4	TAF1	chr7:39662862-39663396	PFSK-1	brain:	n/a	n/a
5	YY1	chr7:39662445-39663523	SK-N-SH_RA	brain:	n/a	chr7:39662807-39662826 chr7:39663473-39663482 chr7:39663474-39663485 chr7:39663040-39663054 chr7:39662812-39662824 chr7:39663146-39663157 chr7:39663477-39663488 chr7:39663495-39663504 chr7:39663498-39663507 chr7:39662802-39662824 chr7:39662813-39662821 chr7:39663476-39663485 chr7:39662815-39662823 chr7:39663028-39663042 chr7:39662814-39662824
6	JUND	chr7:39662456-39663323	H1-hESC	embryonic stem cell:	n/a	chr7:39663142-39663151 chr7:39663137-39663146
7	ZKSCAN1	chr7:39662885-39663325	Hela-S3	cervix:	n/a	n/a
8	ZNF384	chr7:39662884-39663280	K562	blood:	n/a	n/a
9	GABPA	chr7:39662554-39663635	SK-N-SH	brain:	n/a	n/a
10	ELF1	chr7:39662888-39663425	A549	lung:	n/a	chr7:39663035-39663047 chr7:39663153-39663166
11	MAX	chr7:39662446-39663940	ECC-1	luminal epithelium:	n/a	chr7:39662743-39662753 chr7:39662714-39662722
12	YY1	chr7:39662460-39663694	GM12892	blood:	n/a	chr7:39662807-39662826 chr7:39663473-39663482 chr7:39663474-39663485 chr7:39663040-39663054 chr7:39662812-39662824 chr7:39663146-39663157 chr7:39663477-39663488 chr7:39663495-39663504 chr7:39663644-39663655 chr7:39663498-39663507 chr7:39662802-39662824 chr7:39662813-39662821 chr7:39663476-39663485 chr7:39662815-39662823 chr7:39663028-39663042 chr7:39662814-39662824
13	BHLHE40	chr7:39662312-39664819	GM12878	blood:	n/a	chr7:39663497-39663513 chr7:39663776-39663792 chr7:39663770-39663786 chr7:39663467-39663483
14	POLR2A	chr7:39662742-39663361	HepG2	liver:	n/a	n/a
15	YY1	chr7:39662425-39663472	GM12878	blood:	n/a	chr7:39662807-39662826 chr7:39663040-39663054 chr7:39662812-39662824 chr7:39663146-39663157 chr7:39662802-39662824 chr7:39662813-39662821 chr7:39662815-39662823 chr7:39663028-39663042 chr7:39662814-39662824
16	MYBL2	chr7:39662913-39663457	HepG2	liver:	n/a	n/a
17	RELA	chr7:39662726-39664489	GM12891	blood:	n/a	n/a
18	RCOR1	chr7:39662602-39664372	K562	blood:	n/a	n/a
19	GABPA	chr7:39662633-39663630	A549	lung:	n/a	n/a
20	YY1	chr7:39662440-39663868	HepG2	liver:	n/a	chr7:39662807-39662826 chr7:39663473-39663482 chr7:39663474-39663485 chr7:39663040-39663054 chr7:39662812-39662824 chr7:39663146-39663157 chr7:39663477-39663488 chr7:39663495-39663504 chr7:39663644-39663655 chr7:39663498-39663507 chr7:39662802-39662824 chr7:39662813-39662821 chr7:39663476-39663485 chr7:39662815-39662823 chr7:39663028-39663042 chr7:39662814-39662824
21	CEBPB	chr7:39662903-39663867	Hela-S3	cervix:	n/a	n/a
22	EP300	chr7:39662846-39663366	H1-hESC	embryonic stem cell:	n/a	n/a
23	NFIC	chr7:39662828-39663494	ECC-1	luminal epithelium:	n/a	n/a
24	TAF1	chr7:39662633-39663535	A549	lung:	n/a	n/a
25	SIN3A	chr7:39662896-39663694	GM12878	blood:	n/a	n/a
26	EGR1	chr7:39662877-39663317	GM12878	blood:	n/a	chr7:39663037-39663047
27	GABPA	chr7:39662582-39663670	HL-60	blood:	n/a	n/a
28	YY1	chr7:39662577-39663279	HepG2	liver:	n/a	chr7:39662807-39662826 chr7:39663040-39663054 chr7:39662812-39662824 chr7:39663146-39663157 chr7:39662802-39662824 chr7:39662813-39662821 chr7:39662815-39662823 chr7:39663028-39663042 chr7:39662814-39662824
29	POU2F2	chr7:39662457-39663439	GM12878	blood:	n/a	chr7:39663142-39663154
30	POLR2A	chr7:39662408-39663414	GM12891	blood:	n/a	n/a
31	TRIM28	chr7:39662786-39663439	K562	blood:	n/a	n/a
32	NFATC1	chr7:39662696-39663388	GM12878	blood:	n/a	n/a
33	MAZ	chr7:39662486-39663522	HepG2	liver:	n/a	chr7:39662743-39662753 chr7:39662714-39662722
34	ELF1	chr7:39662827-39663491	GM12878	blood:	n/a	chr7:39663035-39663047 chr7:39663474-39663486 chr7:39663473-39663482 chr7:39663153-39663166
35	MXI1	chr7:39662512-39663825	HepG2	liver:	n/a	n/a
36	REST	chr7:39662838-39663330	HepG2	liver:	n/a	chr7:39663136-39663149 chr7:39662958-39662976 chr7:39663151-39663161
37	NFIC	chr7:39662896-39663279	HepG2	liver:	n/a	n/a
38	TCF7L2	chr7:39662393-39663887	Hela-S3	cervix:	n/a	n/a
39	GABPA	chr7:39662866-39663584	K562	blood:	n/a	n/a
40	POLR2A	chr7:39662475-39663875	HepG2	liver:	n/a	n/a
41	SMC3	chr7:39662783-39664395	Hela-S3	cervix:	n/a	chr7:39663028-39663038 chr7:39662853-39662863 chr7:39662856-39662864
42	CTCF	chr7:39662780-39662930	AG04449	skin:	n/a	n/a
43	TAF7	chr7:39662519-39663451	H1-hESC	embryonic stem cell:	n/a	n/a
44	MAX	chr7:39662914-39663375	A549	lung:	n/a	n/a
45	YY1	chr7:39662590-39663179	GM12892	blood:	n/a	chr7:39662807-39662826 chr7:39663040-39663054 chr7:39662812-39662824 chr7:39663146-39663157 chr7:39662802-39662824 chr7:39662813-39662821 chr7:39662815-39662823 chr7:39663028-39663042 chr7:39662814-39662824
46	PML	chr7:39662703-39663455	K562	blood:	n/a	n/a
47	MXI1	chr7:39662169-39663832	GM12878	blood:	n/a	n/a
48	MAX	chr7:39662383-39663972	SK-N-SH	brain:	n/a	chr7:39662743-39662753 chr7:39662714-39662722
49	EP300	chr7:39662873-39663331	SK-N-SH_RA	brain:	n/a	n/a
50	GTF2F1	chr7:39662360-39663365	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:12726248..12727150-chr7:39662597..39663297,2	Hela-S3	cervix:
2	chr7:39649814..39652615-chr7:39661583..39664092,3	MCF-7	breast:
3	chr7:39661595..39664442-chr7:39724184..39727170,2	MCF-7	breast:
4	chr7:39661404..39663086-chr7:39725958..39728030,2	MCF-7	breast:
5	chr7:39603623..39606050-chr7:39662280..39665105,2	MCF-7	breast:
6	chr12:48099025..48099990-chr7:39662730..39663360,2	Hela-S3	cervix:
7	chr17:56735362..56737542-chr7:39660335..39663097,2	MCF-7	breast:
8	chr7:39661332..39663000-chr7:39732479..39734683,2	K562	blood:
9	chr7:39660619..39666370-chr7:39771379..39777121,13	MCF-7	breast:
10	chr14:103988878..103989543-chr7:39662895..39663568,2	Hela-S3	cervix:
11	chr7:39661063..39664836-chr7:39769831..39775766,6	MCF-7	breast:

Variant related genes	Relation type
RALA	TF binding region
ENSG00000241127	Chromatin interaction
ENSG00000006451	Chromatin interaction
ENSG00000257433	Chromatin interaction
ENSG00000231951	Chromatin interaction
ENSG00000188185	Chromatin interaction
ENSG00000122644	Chromatin interaction
ENSG00000005175	Chromatin interaction
ENSG00000227172	Chromatin interaction
ENSG00000166165	Chromatin interaction
ENSG00000202077	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs4723896	0.86[YRI][hapmap]
rs6462941	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs6943083	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73689257	0.86[AFR][1000 genomes]
rs7788924	0.87[YRI][hapmap]
rs7789326	0.87[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv887970	chr7:39587912-39688152	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv508451	chr7:39660784-39787222	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv887971	chr7:39662268-39745775	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 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	chr7:39661600-39663000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr7:39661600-39664600	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr7:39661800-39664400	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr7:39661800-39664600	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr7:39662000-39664200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr7:39662000-39664200	Active TSS	A549	lung
7	chr7:39662000-39664400	Active TSS	H9 Cell Line	embryonic stem cell
8	chr7:39662000-39664400	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr7:39662000-39664600	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr7:39662000-39665200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr7:39662200-39663000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
12	chr7:39662200-39663200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr7:39662200-39663600	Active TSS	Stomach Smooth Muscle	stomach
14	chr7:39662200-39664200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr7:39662200-39664200	Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr7:39662200-39664200	Active TSS	Placenta Amnion	Placenta Amnion
17	chr7:39662200-39664200	Active TSS	Psoas Muscle	Psoas
18	chr7:39662200-39664200	Active TSS	NHEK	skin
19	chr7:39662200-39664400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr7:39662200-39664400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr7:39662200-39664400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr7:39662200-39664600	Active TSS	H1 Cell Line	embryonic stem cell
23	chr7:39662200-39664800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr7:39662200-39664800	Active TSS	HMEC	breast
25	chr7:39662400-39663000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
26	chr7:39662400-39663000	Active TSS	Fetal Heart	heart
27	chr7:39662400-39663200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr7:39662400-39663800	Active TSS	Brain Hippocampus Middle	brain
29	chr7:39662400-39664000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr7:39662400-39664000	Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr7:39662400-39664000	Active TSS	Brain Anterior Caudate	brain
32	chr7:39662400-39664000	Active TSS	Brain Cingulate Gyrus	brain
33	chr7:39662400-39664000	Active TSS	Fetal Brain Male	brain
34	chr7:39662400-39664000	Active TSS	Fetal Lung	lung
35	chr7:39662400-39664000	Active TSS	Pancreas	Pancrea
36	chr7:39662400-39664000	Active TSS	Small Intestine	intestine
37	chr7:39662400-39664200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr7:39662400-39664200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr7:39662400-39664200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr7:39662400-39664200	Active TSS	Fetal Intestine Large	intestine
41	chr7:39662400-39664400	Active TSS	HUES64 Cell Line	embryonic stem cell
42	chr7:39662400-39664400	Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr7:39662400-39664400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr7:39662400-39664400	Active TSS	Aorta	Aorta
45	chr7:39662400-39664400	Active TSS	Colonic Mucosa	Colon
46	chr7:39662400-39664400	Active TSS	Gastric	stomach
47	chr7:39662400-39664400	Active TSS	Lung	lung
48	chr7:39662400-39664400	Active TSS	Ovary	ovary
49	chr7:39662400-39664400	Active TSS	GM12878-XiMat	blood
50	chr7:39662400-39664600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links