Variant report

Variant	rs2702
Chromosome Location	chr8:110651509-110651510
allele	G/T
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:110573084..110574695-chr8:110651484..110652533,12	MCF-7	breast:
2	chr8:110579382..110581964-chr8:110650395..110652048,2	MCF-7	breast:
3	chr8:110649169..110652040-chr8:110653790..110655530,2	K562	blood:
4	chr8:110573673..110575507-chr8:110649898..110652477,2	MCF-7	breast:
5	chr8:110344019..110346826-chr8:110650680..110652185,2	K562	blood:
6	chr8:110643544..110645348-chr8:110650716..110653682,2	MCF-7	breast:
7	chr8:110550837..110554716-chr8:110650281..110652829,3	MCF-7	breast:
8	chr8:110649788..110653968-chr8:110654410..110658481,7	K562	blood:
9	chr8:110645891..110648090-chr8:110649445..110652296,2	K562	blood:
10	chr8:110553979..110556820-chr8:110650989..110652969,2	MCF-7	breast:
11	chr12:52540517..52543405-chr8:110649072..110651646,2	MCF-7	breast:
12	chr8:110650444..110652185-chr8:110656417..110658481,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000147642	Chromatin interaction
ENSG00000147654	Chromatin interaction
ENSG00000248050	Chromatin interaction
ENSG00000120533	Chromatin interaction
ENSG00000120526	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10090145	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10505131	0.94[CEU][hapmap];0.85[JPT][hapmap];0.92[EUR][1000 genomes]
rs10505132	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11774663	0.95[ASN][1000 genomes]
rs11986510	0.91[EUR][1000 genomes]
rs11994796	0.92[EUR][1000 genomes]
rs11998387	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13256586	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13268243	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1573853	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3108829	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108832	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3108837	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3108840	0.88[CEU][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3108853	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3108854	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3108862	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3108863	0.92[EUR][1000 genomes]
rs3108864	0.92[EUR][1000 genomes]
rs3108865	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3108869	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3133926	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3133927	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3133935	0.83[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs3133936	0.87[CEU][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3133937	0.86[ASN][1000 genomes]
rs3134314	0.83[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs3134317	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3134319	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3134325	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3134331	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6469275	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6985646	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7008447	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][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	esv1849702	chr8:110594148-110683804	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2702	PKHD1L1	cis	Lymphoblastoid	GTEx

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:110590200-110654800	Weak transcription	Lung	lung
2	chr8:110620400-110654800	Weak transcription	Esophagus	oesophagus
3	chr8:110621200-110654800	Weak transcription	Fetal Brain Female	brain
4	chr8:110623400-110655000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr8:110626200-110654800	Weak transcription	Brain Anterior Caudate	brain
6	chr8:110629800-110651800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr8:110631600-110652000	Weak transcription	Duodenum Mucosa	Duodenum
8	chr8:110633200-110656000	Weak transcription	Gastric	stomach
9	chr8:110640200-110652000	Weak transcription	Adipose Nuclei	Adipose
10	chr8:110640200-110655200	Weak transcription	Brain Angular Gyrus	brain
11	chr8:110641800-110651600	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr8:110643800-110655400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr8:110646800-110652400	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr8:110647600-110651600	Enhancers	Pancreatic Islets	Pancreatic Islet
15	chr8:110648200-110652000	Enhancers	HepG2	liver
16	chr8:110648200-110655600	Weak transcription	Brain Cingulate Gyrus	brain
17	chr8:110648800-110652000	Weak transcription	Left Ventricle	heart
18	chr8:110649200-110652400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr8:110650400-110652400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr8:110650400-110654800	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr8:110650600-110651600	Enhancers	Liver	Liver
22	chr8:110650600-110651800	Enhancers	NHEK	skin
23	chr8:110650600-110652000	Weak transcription	Pancreas	Pancrea
24	chr8:110650600-110652200	Weak transcription	Colon Smooth Muscle	Colon
25	chr8:110650600-110653800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr8:110650600-110655600	Weak transcription	Right Atrium	heart
27	chr8:110650600-110656200	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr8:110651000-110652400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr8:110651200-110655600	Weak transcription	Fetal Intestine Small	intestine
30	chr8:110651400-110651800	Weak transcription	Fetal Brain Male	brain
31	chr8:110651400-110651800	Weak transcription	Fetal Intestine Large	intestine
32	chr8:110651400-110651800	Weak transcription	Stomach Mucosa	stomach
33	chr8:110651400-110651800	Weak transcription	Stomach Smooth Muscle	stomach
34	chr8:110651400-110652400	Enhancers	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links