Variant report

Variant	rs6963553
Chromosome Location	chr7:139473806-139473807
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr7:139473726-139474852	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr7:139473696-139475134	SK-N-SH	brain:	n/a	n/a
3	NFIC	chr7:139473783-139474933	SK-N-SH	brain:	n/a	n/a
4	GATA3	chr7:139473607-139474975	SK-N-SH	brain:	n/a	chr7:139473659-139473668
5	TCF12	chr7:139473679-139475005	SK-N-SH	brain:	n/a	n/a
6	MXI1	chr7:139473683-139479282	IMR90	lung:	n/a	n/a
7	JUND	chr7:139473791-139474880	SK-N-SH	brain:	n/a	n/a
8	RUNX3	chr7:139473136-139474016	GM12878	blood:	n/a	n/a
9	TCF12	chr7:139473806-139474943	SK-N-SH	brain:	n/a	n/a
10	JUND	chr7:139472599-139474783	SK-N-SH	brain:	n/a	n/a
11	EP300	chr7:139473782-139474947	SK-N-SH	brain:	n/a	chr7:139474302-139474309
12	EP300	chr7:139473753-139474914	SK-N-SH	brain:	n/a	chr7:139474302-139474309

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:139472005..139473850-chr7:139702644..139704624,2	K562	blood:
2	chr7:139473245..139475405-chr7:139553701..139555890,2	K562	blood:
3	chr7:139466166..139468375-chr7:139473040..139475518,2	MCF-7	breast:
4	chr7:139328556..139330958-chr7:139473261..139475609,2	K562	blood:
5	chr7:139468774..139474214-chr7:139474318..139478750,13	MCF-7	breast:
6	chr7:139472264..139474363-chr7:139641675..139643292,2	K562	blood:
7	chr7:139465555..139467223-chr7:139473654..139475179,2	MCF-7	breast:

No data

Variant related genes	Relation type
TBXAS1	TF binding region
ENSG00000064393	Chromatin interaction
ENSG00000059377	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10228448	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10228830	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10252208	1.00[MEX][hapmap]
rs10255449	1.00[MEX][hapmap]
rs10257315	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10257659	0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10261500	1.00[MEX][hapmap]
rs10261622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10261757	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10271046	1.00[MEX][hapmap]
rs10274540	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10278165	0.84[AMR][1000 genomes]
rs17161128	1.00[MEX][hapmap]
rs17161198	1.00[MEX][hapmap]
rs17161200	1.00[MEX][hapmap]
rs17161201	1.00[MEX][hapmap]
rs17161202	1.00[MEX][hapmap]
rs17161230	1.00[MEX][hapmap]
rs17161272	1.00[MEX][hapmap]
rs1859568	1.00[MEX][hapmap]
rs2158667	1.00[MEX][hapmap]
rs4529	1.00[MEX][hapmap]
rs60526073	0.90[AFR][1000 genomes]
rs6947799	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6954520	1.00[MEX][hapmap]
rs6963499	1.00[MEX][hapmap]
rs6964028	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6972460	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73735621	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7455629	0.90[YRI][hapmap];0.88[AFR][1000 genomes]
rs7777901	1.00[MEX][hapmap]
rs7810177	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020234	chr7:139377822-139661964	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1032711	chr7:139411404-139684043	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv464732	chr7:139424022-139654256	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv608472	chr7:139424022-139654256	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1018712	chr7:139429703-139658014	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:139440600-139474600	Weak transcription	Fetal Brain Male	brain
2	chr7:139446600-139475800	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr7:139446600-139476400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:139446800-139476400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr7:139454200-139474000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr7:139455000-139475000	Weak transcription	Fetal Intestine Small	intestine
7	chr7:139459600-139474400	Weak transcription	Fetal Intestine Large	intestine
8	chr7:139463600-139475000	Weak transcription	Ovary	ovary
9	chr7:139465600-139475000	Enhancers	Brain Substantia Nigra	brain
10	chr7:139467600-139475400	Weak transcription	Aorta	Aorta
11	chr7:139467800-139475000	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr7:139468000-139475800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr7:139468200-139474800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr7:139468600-139474200	Weak transcription	K562	blood
15	chr7:139468800-139474200	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr7:139468800-139474800	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr7:139468800-139475000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr7:139468800-139475000	Weak transcription	Placenta	Placenta
19	chr7:139468800-139475600	Enhancers	Primary T cells from cord blood	blood
20	chr7:139469000-139475000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr7:139469000-139475400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr7:139469000-139475600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr7:139469200-139474800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr7:139469200-139474800	Weak transcription	Colonic Mucosa	Colon
25	chr7:139469200-139474800	Weak transcription	Fetal Muscle Leg	muscle
26	chr7:139469200-139475400	Weak transcription	Fetal Muscle Trunk	muscle
27	chr7:139469200-139475800	Weak transcription	Esophagus	oesophagus
28	chr7:139469200-139476200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr7:139469200-139476400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr7:139469600-139474800	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr7:139469600-139475200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr7:139469800-139475800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr7:139470000-139475000	Weak transcription	Fetal Stomach	stomach
34	chr7:139470200-139475200	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr7:139470400-139474400	Enhancers	Brain Hippocampus Middle	brain
36	chr7:139470400-139475000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr7:139470400-139475400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr7:139470600-139475600	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr7:139471000-139474600	Enhancers	Adipose Nuclei	Adipose
40	chr7:139471000-139474600	Genic enhancers	HepG2	liver
41	chr7:139471400-139475800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr7:139471600-139474200	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr7:139471600-139475800	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr7:139471800-139474200	Enhancers	Gastric	stomach
45	chr7:139471800-139474800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr7:139471800-139475400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr7:139472000-139474000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr7:139472000-139474200	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr7:139472000-139475200	Enhancers	HMEC	breast
50	chr7:139472000-139475400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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