Variant report

Variant	rs557656346
Chromosome Location	chr7:39662348-39662349
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	BHLHE40	chr7:39662312-39664819	GM12878	blood:	n/a	chr7:39663497-39663513 chr7:39663776-39663792 chr7:39663770-39663786 chr7:39663467-39663483
2	ZNF384	chr7:39662208-39662550	K562	blood:	n/a	n/a
3	MXI1	chr7:39662169-39663832	GM12878	blood:	n/a	n/a
4	EP300	chr7:39662267-39662783	GM12878	blood:	n/a	n/a
5	POLR2A	chr7:39662305-39663855	NB4	blood:	n/a	n/a
6	REST	chr7:39662205-39664044	H1-neurons	neurons:	n/a	chr7:39663136-39663149 chr7:39662958-39662976 chr7:39663151-39663161
7	POLR2A	chr7:39661358-39663450	K562	blood:	n/a	n/a
8	POLR2A	chr7:39661360-39663434	K562	blood:	n/a	n/a
9	POLR2A	chr7:39661961-39663605	U87	brain:	n/a	n/a
10	POLR2A	chr7:39662259-39663436	GM12892	blood:	n/a	n/a
11	POLR2A	chr7:39659839-39663493	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr7:39660809-39665213	IMR90	lung:	n/a	n/a
13	POLR2A	chr7:39661586-39663615	PANC-1	pancreas:	n/a	n/a
14	TBP	chr7:39662271-39663350	GM12878	blood:	n/a	n/a
15	WRNIP1	chr7:39661909-39662848	GM12878	blood:	n/a	n/a
16	POLR2A	chr7:39661268-39663897	GM12878	blood:	n/a	n/a
17	GABPA	chr7:39662271-39663736	MCF-7	breast:	n/a	n/a
18	POLR2A	chr7:39662335-39663548	GM12892	blood:	n/a	n/a
19	FOXM1	chr7:39662337-39663386	GM12878	blood:	n/a	n/a
20	MTA3	chr7:39662084-39663445	GM12878	blood:	n/a	n/a
21	EBF1	chr7:39662246-39663403	GM12878	blood:	n/a	chr7:39662689-39662700
22	RELA	chr7:39662162-39663417	GM15510	blood:	n/a	n/a
23	POLR2A	chr7:39661250-39663630	SK-N-MC	brain:	n/a	n/a
24	POLR2A	chr7:39662060-39663791	HepG2	liver:	n/a	n/a
25	TCF12	chr7:39662305-39663436	A549	lung:	n/a	chr7:39663129-39663139
26	POLR2A	chr7:39662024-39663264	HepG2	liver:	n/a	n/a
27	YY1	chr7:39662286-39663749	SK-N-SH	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 chr7:39663644-39663655 chr7:39663498-39663507 chr7:39662802-39662824 chr7:39662813-39662821 chr7:39663476-39663485 chr7:39662815-39662823 chr7:39663028-39663042 chr7:39662814-39662824
28	TCF12	chr7:39662300-39662848	ECC-1	luminal epithelium:	n/a	n/a
29	MAZ	chr7:39661407-39664395	K562	blood:	n/a	chr7:39662743-39662753 chr7:39662714-39662722
30	POLR2A	chr7:39661351-39664265	HepG2	liver:	n/a	n/a
31	MYC	chr7:39662152-39663814	NB4	blood:	n/a	chr7:39662743-39662753 chr7:39662714-39662722
32	POLR2A	chr7:39662240-39664408	GM12892	blood:	n/a	n/a
33	TBL1XR1	chr7:39662310-39663456	GM12878	blood:	n/a	n/a
34	ARID3A	chr7:39661542-39662375	K562	blood:	n/a	n/a
35	POLR2A	chr7:39662335-39663538	K562	blood:	n/a	n/a
36	POLR2A	chr7:39662344-39663457	GM12891	blood:	n/a	n/a
37	POLR2A	chr7:39661394-39663507	GM12878	blood:	n/a	n/a
38	POLR2A	chr7:39662290-39663443	GM12891	blood:	n/a	n/a
39	ELF1	chr7:39662320-39663514	MCF-7	breast:	n/a	chr7:39663496-39663508 chr7:39663035-39663047 chr7:39663474-39663486 chr7:39663473-39663482 chr7:39663495-39663504 chr7:39663153-39663166
40	SMARCC1	chr7:39662034-39664405	Hela-S3	cervix:	n/a	n/a
41	EBF1	chr7:39662338-39663868	GM12878	blood:	n/a	chr7:39662689-39662700
42	JUND	chr7:39661325-39665588	K562	blood:	n/a	chr7:39664844-39664855 chr7:39664121-39664130 chr7:39663142-39663151 chr7:39663137-39663146
43	MYC	chr7:39662174-39663985	K562	blood:	n/a	chr7:39662743-39662753 chr7:39662714-39662722
44	ZNF263	chr7:39662102-39664478	HEK293-T-REx	kidney:	n/a	chr7:39663246-39663267 chr7:39662836-39662845 chr7:39663812-39663821
45	POLR2A	chr7:39661367-39663802	GM18505	blood:	n/a	n/a
46	MXI1	chr7:39662261-39664403	IMR90	lung:	n/a	n/a
47	MAX	chr7:39662283-39663852	A549	lung:	n/a	chr7:39662743-39662753 chr7:39662714-39662722
48	POLR2A	chr7:39661392-39664433	GM12878	blood:	n/a	n/a
49	POLR2A	chr7:39661434-39663828	K562	blood:	n/a	n/a
50	POLR2A	chr7:39657726-39663410	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:39616830..39619300-chr7:39660316..39662885,2	K562	blood:
2	chr7:39649814..39652615-chr7:39661583..39664092,3	MCF-7	breast:
3	chr7:39652942..39654975-chr7:39661144..39662912,2	MCF-7	breast:
4	chr7:39661595..39664442-chr7:39724184..39727170,2	MCF-7	breast:
5	chr7:39661404..39663086-chr7:39725958..39728030,2	MCF-7	breast:
6	chr7:39603623..39606050-chr7:39662280..39665105,2	MCF-7	breast:
7	chr7:39660516..39662861-chr7:39772033..39774524,2	K562	blood:
8	chr17:56735362..56737542-chr7:39660335..39663097,2	MCF-7	breast:
9	chr7:39661332..39663000-chr7:39732479..39734683,2	K562	blood:
10	chr7:39660619..39666370-chr7:39771379..39777121,13	MCF-7	breast:
11	chr7:39635256..39637997-chr7:39660350..39662905,2	MCF-7	breast:
12	chr7:39643128..39644638-chr7:39660434..39662671,2	MCF-7	breast:
13	chr7:39661063..39664836-chr7:39769831..39775766,6	MCF-7	breast:

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

Extended variants
information (count: 3 )
Associated
traits (count: 0)

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:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39658000-39662400	Weak transcription	Esophagus	oesophagus
2	chr7:39660400-39662400	Enhancers	Primary hematopoietic stem cells	blood
3	chr7:39661000-39662400	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr7:39661000-39662400	Enhancers	Primary B cells from peripheral blood	blood
5	chr7:39661200-39662400	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr7:39661200-39662600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr7:39661200-39662800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
8	chr7:39661400-39662400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr7:39661400-39662600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr7:39661400-39662800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr7:39661400-39662800	Flanking Active TSS	NH-A	brain
12	chr7:39661600-39662400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr7:39661600-39662400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr7:39661600-39662400	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr7:39661600-39662400	Weak transcription	Spleen	Spleen
16	chr7:39661600-39662400	Flanking Active TSS	GM12878-XiMat	blood
17	chr7:39661600-39662400	Flanking Active TSS	NHLF	lung
18	chr7:39661600-39662600	Flanking Active TSS	Dnd41	blood
19	chr7:39661600-39662600	Flanking Active TSS	K562	blood
20	chr7:39661600-39662800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr7:39661600-39663000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr7:39661600-39664600	Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr7:39661800-39662400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr7:39661800-39662400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr7:39661800-39662400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr7:39661800-39662400	Enhancers	Small Intestine	intestine
27	chr7:39661800-39662400	Flanking Active TSS	HepG2	liver
28	chr7:39661800-39662600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr7:39661800-39662600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr7:39661800-39662600	Flanking Active TSS	HSMM	muscle
31	chr7:39661800-39662600	Flanking Active TSS	HSMMtube	muscle
32	chr7:39661800-39662800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
33	chr7:39661800-39664400	Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr7:39661800-39664600	Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr7:39662000-39662400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr7:39662000-39662400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr7:39662000-39662400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
38	chr7:39662000-39662400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr7:39662000-39662400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr7:39662000-39662400	Enhancers	Primary T cells fromperipheralblood	blood
41	chr7:39662000-39662400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr7:39662000-39662400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr7:39662000-39662400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr7:39662000-39662400	Weak transcription	Pancreas	Pancrea
45	chr7:39662000-39662400	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr7:39662000-39662600	Flanking Active TSS	Liver	Liver
47	chr7:39662000-39662600	Active TSS	Brain Germinal Matrix	brain
48	chr7:39662000-39662600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
49	chr7:39662000-39662600	Flanking Active TSS	Duodenum Mucosa	Duodenum
50	chr7:39662000-39662600	Flanking Active TSS	Fetal Intestine Small	intestine

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