Variant report

Variant	rs7540898
Chromosome Location	chr1:173473957-173473958
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:173446841..173450176-chr1:173473892..173477707,4	K562	blood:
2	chr1:173445909..173448174-chr1:173472992..173475545,2	MCF-7	breast:
3	chr1:173471541..173474738-chr1:173476002..173477727,3	MCF-7	breast:
4	chr1:173455943..173458874-chr1:173472089..173474445,2	MCF-7	breast:
5	chr1:173444700..173449124-chr1:173472471..173476984,5	MCF-7	breast:
6	chr1:173454021..173455524-chr1:173471878..173474498,2	K562	blood:
7	chr1:173445753..173447978-chr1:173472675..173475693,4	K562	blood:

Variant related genes	Relation type
ENSG00000117592	Chromatin interaction

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

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

rs_ID	r²[population]
rs10082296	0.88[YRI][hapmap];1.00[AMR][1000 genomes]
rs10128064	1.00[AMR][1000 genomes]
rs10158274	1.00[AMR][1000 genomes]
rs10159349	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs12239406	1.00[AMR][1000 genomes]
rs13313018	1.00[AMR][1000 genomes]
rs13374735	1.00[AMR][1000 genomes]
rs13375569	1.00[AMR][1000 genomes]
rs13376081	1.00[AMR][1000 genomes]
rs13376339	1.00[AMR][1000 genomes]
rs13376392	1.00[AMR][1000 genomes]
rs13376447	1.00[AMR][1000 genomes]
rs34683148	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35052032	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35133735	1.00[AMR][1000 genomes]
rs6425252	1.00[AMR][1000 genomes]
rs6656810	1.00[AMR][1000 genomes]
rs6665497	0.89[YRI][hapmap];1.00[AMR][1000 genomes]
rs6695916	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6703355	1.00[AMR][1000 genomes]
rs7518933	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7532991	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831915	chr1:173268424-173482157	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173448000-173477000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:173458600-173475600	Weak transcription	Fetal Kidney	kidney
3	chr1:173458600-173476600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:173459400-173474000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:173459400-173475400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr1:173466400-173475400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:173471000-173474200	Enhancers	Liver	Liver
8	chr1:173472400-173474000	Enhancers	Stomach Smooth Muscle	stomach
9	chr1:173472600-173474000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:173472800-173474800	Weak transcription	HSMMtube	muscle
11	chr1:173472800-173475400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:173473000-173474000	Enhancers	Fetal Brain Female	brain
13	chr1:173473200-173475400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:173473200-173475800	Weak transcription	NHLF	lung
15	chr1:173473200-173476200	Weak transcription	Colon Smooth Muscle	Colon
16	chr1:173473200-173476200	Weak transcription	K562	blood
17	chr1:173473200-173476600	Weak transcription	NHDF-Ad	bronchial
18	chr1:173473400-173475600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:173473600-173474000	Weak transcription	Fetal Brain Male	brain
20	chr1:173473600-173476600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr1:173473800-173474800	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr1:173473800-173475400	Weak transcription	Adipose Nuclei	Adipose
23	chr1:173473800-173475400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr1:173473800-173475400	Weak transcription	Stomach Mucosa	stomach
25	chr1:173473800-173476600	Enhancers	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links