Variant report

Variant	rs10228105
Chromosome Location	chr7:26734509-26734510
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:26730354..26732072-chr7:26734389..26737232,2	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1391805	0.90[TSI][hapmap]
rs1548481	0.81[YRI][hapmap]
rs212853	0.84[ASW][hapmap];0.95[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs212855	0.93[AFR][1000 genomes]
rs490366	0.90[TSI][hapmap]
rs550141	0.89[TSI][hapmap]
rs6975813	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7782659	0.93[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029596	chr7:26302739-26737913	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv538804	chr7:26302739-26737913	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1025538	chr7:26482342-27376045	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
4	nsv538805	chr7:26482342-27376045	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	nsv830929	chr7:26587888-26749735	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv5672	chr7:26711462-26757891	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10228105	HOXA9	cis	parietal	SCAN
rs10228105	NFE2L3	cis	parietal	SCAN
rs10228105	TRIL	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26705000-26759600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr7:26724400-26742000	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr7:26727200-26735600	Weak transcription	Esophagus	oesophagus
4	chr7:26727200-26739200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr7:26728600-26734600	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr7:26729000-26756400	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr7:26729200-26747000	Weak transcription	Primary B cells from cord blood	blood
8	chr7:26729200-26747000	Weak transcription	Primary B cells from peripheral blood	blood
9	chr7:26729400-26737000	Weak transcription	Psoas Muscle	Psoas
10	chr7:26729600-26738800	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr7:26729600-26750000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr7:26729800-26738000	Weak transcription	A549	lung
13	chr7:26730000-26743800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr7:26730000-26747000	Weak transcription	Fetal Kidney	kidney
15	chr7:26730400-26735200	Weak transcription	NHLF	lung
16	chr7:26730400-26739400	Weak transcription	Adipose Nuclei	Adipose
17	chr7:26730400-26739800	Weak transcription	Fetal Intestine Small	intestine
18	chr7:26730400-26740200	Weak transcription	Fetal Intestine Large	intestine
19	chr7:26730600-26735400	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr7:26730600-26739800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr7:26731800-26734600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr7:26731800-26737800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr7:26731800-26743800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr7:26731800-26779200	Weak transcription	Spleen	Spleen
25	chr7:26732200-26735400	Weak transcription	Fetal Muscle Leg	muscle
26	chr7:26732200-26744600	Weak transcription	Primary hematopoietic stem cells	blood
27	chr7:26732200-26765000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr7:26732400-26740000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr7:26733000-26736600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr7:26733400-26734800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr7:26734200-26734800	Enhancers	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links