Variant report

Variant	rs13235723
Chromosome Location	chr7:33292909-33292910
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:41463874..41467729-chr7:33291332..33294337,4	K562	blood:
2	chr17:41380312..41383401-chr7:33291355..33294353,3	MCF-7	breast:
3	chr17:41380387..41382197-chr7:33292837..33294355,4	MCF-7	breast:
4	chr17:41462939..41465367-chr7:33292835..33294355,2	MCF-7	breast:
5	chr17:41398797..41401165-chr7:33291335..33294355,5	MCF-7	breast:
6	chr17:41380292..41383703-chr7:33291335..33294335,6	K562	blood:
7	chr17:41398400..41401723-chr7:33291352..33294335,3	K562	blood:
8	chr17:41380127..41383362-chr7:33291332..33294355,8	K562	blood:
9	chr17:41398400..41402313-chr7:33292833..33294335,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000188825	Chromatin interaction
ENSG00000236383	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10224956	1.00[JPT][hapmap]
rs10227739	1.00[JPT][hapmap]
rs10232564	1.00[JPT][hapmap]
rs10240165	0.90[JPT][hapmap]
rs10240664	1.00[JPT][hapmap]
rs10241188	1.00[JPT][hapmap]
rs10269937	1.00[JPT][hapmap]
rs10270961	1.00[JPT][hapmap]
rs10272253	1.00[JPT][hapmap]
rs10278228	0.90[JPT][hapmap]
rs10486525	0.94[YRI][hapmap];0.84[AFR][1000 genomes]
rs10951376	1.00[JPT][hapmap]
rs10951377	1.00[JPT][hapmap]
rs10951380	1.00[JPT][hapmap]
rs10951381	1.00[JPT][hapmap]
rs1117311	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11760829	1.00[JPT][hapmap]
rs11763306	1.00[JPT][hapmap]
rs11766506	1.00[JPT][hapmap]
rs11766521	1.00[JPT][hapmap]
rs11769811	1.00[JPT][hapmap]
rs12666753	1.00[JPT][hapmap]
rs12671396	1.00[JPT][hapmap]
rs12673026	0.90[JPT][hapmap]
rs12701289	1.00[JPT][hapmap]
rs13224392	0.90[JPT][hapmap]
rs13227275	1.00[JPT][hapmap]
rs13236414	1.00[JPT][hapmap]
rs13236865	1.00[JPT][hapmap]
rs13240884	1.00[JPT][hapmap]
rs13244450	1.00[JPT][hapmap]
rs1362367	1.00[JPT][hapmap]
rs1362370	0.84[YRI][hapmap]
rs1406606	1.00[JPT][hapmap]
rs1468797	1.00[JPT][hapmap]
rs1548879	1.00[JPT][hapmap]
rs1569239	1.00[JPT][hapmap]
rs17150810	1.00[JPT][hapmap]
rs17169835	1.00[JPT][hapmap]
rs17169847	1.00[JPT][hapmap]
rs17169855	1.00[JPT][hapmap]
rs17169881	1.00[JPT][hapmap]
rs17169913	1.00[JPT][hapmap]
rs17170138	0.84[AFR][1000 genomes]
rs17170140	0.94[YRI][hapmap];0.84[AFR][1000 genomes]
rs17170142	1.00[JPT][hapmap]
rs17170143	0.84[AFR][1000 genomes]
rs17170145	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17170155	0.84[AFR][1000 genomes]
rs17170174	1.00[JPT][hapmap]
rs17170175	1.00[JPT][hapmap]
rs1861298	1.00[JPT][hapmap]
rs2160253	1.00[JPT][hapmap]
rs34950347	0.84[AFR][1000 genomes]
rs4628178	0.83[YRI][hapmap]
rs4720103	1.00[JPT][hapmap]
rs4720104	1.00[JPT][hapmap]
rs4720105	1.00[JPT][hapmap]
rs4720106	1.00[JPT][hapmap]
rs4720107	1.00[JPT][hapmap]
rs4723255	1.00[JPT][hapmap]
rs4723256	1.00[JPT][hapmap]
rs4723257	1.00[JPT][hapmap]
rs4723258	1.00[JPT][hapmap]
rs4723259	1.00[JPT][hapmap]
rs4723260	1.00[JPT][hapmap]
rs55865959	0.82[AFR][1000 genomes]
rs60268357	0.84[AFR][1000 genomes]
rs6944559	0.90[YRI][hapmap];0.82[AFR][1000 genomes]
rs6952244	0.94[YRI][hapmap];0.84[AFR][1000 genomes]
rs6952877	1.00[JPT][hapmap]
rs6953348	1.00[JPT][hapmap]
rs6969284	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs6973114	0.89[YRI][hapmap]
rs6973552	0.94[YRI][hapmap];0.84[AFR][1000 genomes]
rs73307398	0.84[AFR][1000 genomes]
rs73307399	0.84[AFR][1000 genomes]
rs73307400	0.84[AFR][1000 genomes]
rs73309308	0.84[AFR][1000 genomes]
rs73309310	0.84[AFR][1000 genomes]
rs73309312	0.84[AFR][1000 genomes]
rs73309316	0.84[AFR][1000 genomes]
rs73309318	0.84[AFR][1000 genomes]
rs73309324	0.82[AFR][1000 genomes]
rs73688093	0.84[AFR][1000 genomes]
rs764127	1.00[JPT][hapmap]
rs7777101	1.00[JPT][hapmap]
rs7783612	1.00[JPT][hapmap]
rs7793667	0.82[AFR][1000 genomes]
rs7793862	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7798118	0.93[YRI][hapmap];0.84[AFR][1000 genomes]
rs7804742	1.00[JPT][hapmap]
rs7808472	0.82[AFR][1000 genomes]
rs7809235	0.88[YRI][hapmap]
rs7810388	1.00[JPT][hapmap]
rs9638888	1.00[JPT][hapmap]
rs9638889	1.00[JPT][hapmap]
rs986554	1.00[JPT][hapmap]
rs987501	1.00[JPT][hapmap]
rs9886317	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830943	chr7:33167106-33352759	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
2	nsv606610	chr7:33218763-33486316	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1016416	chr7:33241443-33559477	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv916660	chr7:33272493-33506384	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13235723	HERPUD2	cis	parietal	SCAN
rs13235723	BBS9	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:33283800-33316000	Weak transcription	Ovary	ovary
2	chr7:33287200-33296000	Weak transcription	Pancreas	Pancrea
3	chr7:33287800-33293600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr7:33288800-33317600	Weak transcription	Gastric	stomach
5	chr7:33289400-33309000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr7:33289600-33310800	Weak transcription	Psoas Muscle	Psoas
7	chr7:33290000-33316200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr7:33290800-33295800	Weak transcription	Fetal Lung	lung
9	chr7:33290800-33309000	Weak transcription	Fetal Stomach	stomach
10	chr7:33290800-33316400	Weak transcription	Aorta	Aorta
11	chr7:33291200-33293000	Weak transcription	NHLF	lung
12	chr7:33291200-33297600	Weak transcription	Osteobl	bone
13	chr7:33291200-33297800	Weak transcription	Colon Smooth Muscle	Colon
14	chr7:33291200-33298000	Weak transcription	NHDF-Ad	bronchial
15	chr7:33291200-33316000	Weak transcription	Primary T cells from cord blood	blood
16	chr7:33291600-33305200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr7:33291800-33307600	Weak transcription	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links