Variant report

Variant	rs28429588
Chromosome Location	chr7:128085002-128085003
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	GATA3	chr7:128083913-128085115	T-47D	breast:	n/a	chr7:128084297-128084308 chr7:128084781-128084792
2	TCF12	chr7:128084216-128085239	MCF-7	breast:	n/a	n/a
3	HDAC2	chr7:128084207-128085172	MCF-7	breast:	n/a	n/a
4	MAX	chr7:128084114-128085117	MCF-7	breast:	n/a	n/a
5	REST	chr7:128084829-128085161	MCF-7	breast:	n/a	n/a
6	JUND	chr7:128084279-128085136	T-47D	breast:	n/a	chr7:128084457-128084468
7	ZNF217	chr7:128084832-128085079	MCF-7	breast:	n/a	n/a
8	GATA3	chr7:128084002-128085198	MCF-7	breast:	n/a	chr7:128084297-128084308 chr7:128084781-128084792
9	NR2F2	chr7:128083732-128085175	MCF-7	breast:	n/a	chr7:128084265-128084280
10	FOXA1	chr7:128084208-128085152	T-47D	breast:	n/a	n/a
11	GATA3	chr7:128083927-128085178	T-47D	breast:	n/a	chr7:128084297-128084308 chr7:128084781-128084792
12	EP300	chr7:128083996-128085196	T-47D	breast:	n/a	n/a
13	EP300	chr7:128084143-128085182	T-47D	breast:	n/a	n/a
14	FOXA1	chr7:128084190-128085156	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:128066861..128069656-chr7:128084982..128087017,2	MCF-7	breast:
2	chr7:128071934..128079559-chr7:128081793..128086197,10	MCF-7	breast:
3	chr7:128082541..128090035-chr7:128090151..128101015,22	MCF-7	breast:
4	chr7:128081121..128082834-chr7:128084423..128086408,3	K562	blood:
5	chr7:128084340..128085860-chr7:128086520..128088329,2	MCF-7	breast:
6	chr7:128083686..128086427-chr7:128093165..128095584,3	K562	blood:

Variant related genes	Relation type
RNU7-54P	TF binding region
ENSG00000273184	Chromatin interaction
ENSG00000135245	Chromatin interaction
ENSG00000240758	Chromatin interaction
ENSG00000228700	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10228542	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10239919	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10247945	0.82[EUR][1000 genomes]
rs11562031	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12111997	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12113427	0.82[EUR][1000 genomes]
rs1560215	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17152065	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28391244	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4731449	0.82[EUR][1000 genomes]
rs57075087	0.86[EUR][1000 genomes]
rs6978246	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72624928	0.86[EUR][1000 genomes]
rs7779455	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7779818	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7779945	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7781310	0.81[EUR][1000 genomes]
rs7783540	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7784120	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7784564	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7806193	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831124	chr7:127970345-128147910	Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
2	nsv608401	chr7:128083454-128108776	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128051400-128086200	Weak transcription	Right Atrium	heart
2	chr7:128075600-128093800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr7:128075600-128093800	Weak transcription	Pancreas	Pancrea
4	chr7:128078600-128095200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr7:128079400-128085800	Weak transcription	K562	blood
6	chr7:128081400-128085200	Enhancers	Fetal Intestine Large	intestine
7	chr7:128081400-128085600	Enhancers	Fetal Intestine Small	intestine
8	chr7:128083400-128085800	Enhancers	Placenta	Placenta
9	chr7:128083800-128085200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr7:128083800-128085200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr7:128083800-128085200	Enhancers	NHEK	skin
12	chr7:128084000-128090000	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr7:128084200-128086200	Weak transcription	Fetal Muscle Trunk	muscle
14	chr7:128084400-128086000	Weak transcription	Fetal Muscle Leg	muscle
15	chr7:128084400-128088800	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr7:128084600-128095800	Weak transcription	Gastric	stomach
17	chr7:128084800-128086000	Weak transcription	Adipose Nuclei	Adipose
18	chr7:128084800-128086200	Weak transcription	A549	lung
19	chr7:128084800-128086400	Weak transcription	Duodenum Mucosa	Duodenum
20	chr7:128084800-128092000	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr7:128084800-128093600	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr7:128084800-128093800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr7:128085000-128088000	Weak transcription	GM12878-XiMat	blood

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