Variant report

Variant	rs10228088
Chromosome Location	chr7:16825791-16825792
allele	A/C
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	chr7:16825415-16826196	MCF-7	breast:	n/a	chr7:16826105-16826115
2	GATA3	chr7:16825637-16825820	SH-SY5Y	brain:	n/a	n/a
3	GATA2	chr7:16825484-16825861	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:16792019..16795957-chr7:16825471..16827431,5	MCF-7	breast:
2	chr7:16825159..16826158-chr7:16919904..16920435,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000267906	TF binding region
ENSG00000106537	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10224098	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10227514	1.00[CEU][hapmap]
rs10228338	1.00[CEU][hapmap]
rs10237800	1.00[CEU][hapmap]
rs10260136	1.00[CEU][hapmap]
rs10273406	1.00[CEU][hapmap]
rs10275921	1.00[CEU][hapmap]
rs10280750	1.00[CEU][hapmap]
rs10282680	1.00[ASW][hapmap];1.00[CEU][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]
rs11976539	1.00[CEU][hapmap]
rs2177784	1.00[CEU][hapmap]
rs28569833	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6957388	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6968207	1.00[CEU][hapmap]
rs706035	1.00[CHD][hapmap]
rs73073538	1.00[AMR][1000 genomes]
rs7777674	1.00[CEU][hapmap]
rs7802611	1.00[CEU][hapmap]
rs818492	1.00[CEU][hapmap]
rs818582	1.00[CEU][hapmap]
rs818584	1.00[CEU][hapmap]
rs9690166	1.00[CEU][hapmap]

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	nsv1028125	chr7:16529160-16847225	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1024059	chr7:16639432-16836425	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:16795000-16828400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr7:16805000-16832400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr7:16811400-16833600	Weak transcription	Fetal Muscle Leg	muscle
4	chr7:16814000-16834600	Weak transcription	Fetal Brain Male	brain
5	chr7:16814200-16826400	Weak transcription	Right Ventricle	heart
6	chr7:16814400-16843800	Weak transcription	Small Intestine	intestine
7	chr7:16815000-16838000	Weak transcription	K562	blood
8	chr7:16816800-16835000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr7:16818600-16829000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr7:16819000-16830600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr7:16819800-16838000	Weak transcription	Placenta	Placenta
12	chr7:16820000-16825800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr7:16820000-16827600	Strong transcription	Primary B cells from peripheral blood	blood
14	chr7:16820200-16835400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr7:16820800-16827400	Strong transcription	Primary B cells from cord blood	blood
16	chr7:16822600-16829600	Weak transcription	NH-A	brain
17	chr7:16823400-16826800	Weak transcription	Duodenum Mucosa	Duodenum
18	chr7:16823400-16830000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr7:16823600-16829400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr7:16823600-16835400	Weak transcription	Primary hematopoietic stem cells	blood
21	chr7:16823600-16843600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr7:16823800-16826800	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr7:16824800-16825800	Enhancers	Fetal Lung	lung
24	chr7:16825000-16825800	Enhancers	Fetal Brain Female	brain
25	chr7:16825000-16825800	Enhancers	Placenta Amnion	Placenta Amnion
26	chr7:16825000-16825800	Enhancers	Stomach Mucosa	stomach
27	chr7:16825000-16826000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr7:16825000-16826000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr7:16825200-16828800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr7:16825400-16825800	Strong transcription	Left Ventricle	heart
31	chr7:16825400-16825800	Enhancers	HSMMtube	muscle
32	chr7:16825400-16828600	Enhancers	Fetal Intestine Large	intestine
33	chr7:16825600-16825800	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr7:16825600-16825800	Enhancers	Fetal Stomach	stomach
35	chr7:16825600-16825800	Genic enhancers	Gastric	stomach
36	chr7:16825600-16825800	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr7:16825600-16826400	Enhancers	A549	lung
38	chr7:16825600-16828000	Enhancers	Fetal Intestine Small	intestine

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