Variant report

Variant	rs2236628
Chromosome Location	chr8:110598198-110598199
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:110595759..110598292-chr8:110656229..110657746,2	MCF-7	breast:
2	chr8:110588060..110591053-chr8:110594927..110598515,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000147642	Chromatin interaction
ENSG00000248050	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10088258	1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs10088612	0.83[ASN][1000 genomes]
rs10088684	0.83[ASN][1000 genomes]
rs1009371	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs10108943	0.91[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs10111682	1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs1013482	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs1026437	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs1044230	1.00[CHB][hapmap];0.81[CHD][hapmap];0.83[JPT][hapmap];0.92[ASN][1000 genomes]
rs10505133	0.95[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs13249244	0.81[ASN][1000 genomes]
rs13439318	0.83[ASN][1000 genomes]
rs13439864	0.95[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs1379361	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs1379366	0.91[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs1379367	0.95[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs1457282	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs1457288	0.91[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs1457294	0.95[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs1457295	0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs1563578	0.95[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs1563580	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs1617259	0.95[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs1617350	0.83[ASN][1000 genomes]
rs1630134	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs1630942	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs1673383	0.95[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs1673384	0.95[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs1673386	1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs1673389	0.95[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs1673395	0.95[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs1673399	0.95[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs1673409	0.95[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs1673410	0.95[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs1673411	0.91[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs1673412	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs1673413	0.95[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs1673415	0.91[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs1673416	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs1673419	0.91[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs1673420	0.94[CHB][hapmap];0.80[JPT][hapmap];0.80[ASN][1000 genomes]
rs1673421	0.85[CHB][hapmap]
rs1673422	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs1673426	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs1673427	0.81[ASN][1000 genomes]
rs1673428	0.95[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs17377636	0.81[ASN][1000 genomes]
rs17449762	0.81[ASN][1000 genomes]
rs1783140	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs1783141	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs1783147	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs1783148	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs1783153	0.85[CHB][hapmap];0.80[ASN][1000 genomes]
rs1783154	0.91[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs1783157	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs1783158	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs1783159	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs1783162	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs1783166	0.91[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs1783167	0.81[ASN][1000 genomes]
rs1783168	0.91[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs1783169	1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs1783170	0.86[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs1783171	0.95[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs1783172	0.90[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs1783173	1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs1783174	0.95[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs1783175	0.81[ASN][1000 genomes]
rs1892759	0.94[JPT][hapmap]
rs1892760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2022934	0.91[CHB][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs2022935	1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs2154658	0.94[JPT][hapmap]
rs2154660	0.95[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs2236627	0.86[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs2607624	0.95[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs2607625	0.95[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs2607627	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs2607628	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs2607629	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs2607630	0.89[CHB][hapmap];0.80[JPT][hapmap]
rs2607631	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs2607633	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs2607635	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs2703377	1.00[CHB][hapmap];0.81[CHD][hapmap];0.92[ASN][1000 genomes]
rs2703382	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2703384	0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2703386	0.91[CHB][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs2703387	0.92[ASN][1000 genomes]
rs2703388	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2703389	1.00[CHB][hapmap];0.83[JPT][hapmap];0.92[ASN][1000 genomes]
rs2844231	0.86[CHB][hapmap];0.81[CHD][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs2844234	0.90[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.83[JPT][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2844235	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844236	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844254	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs2844257	0.95[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs2844258	0.95[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs2844259	0.95[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs2844260	1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs2844261	0.95[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs3808380	0.80[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs4529437	1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs7006166	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs7011340	0.95[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs7011803	1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs720139	0.80[ASN][1000 genomes]
rs720140	0.80[ASN][1000 genomes]
rs730885	1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs753995	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs7818726	0.89[ASN][1000 genomes]
rs7821242	0.81[ASN][1000 genomes]
rs897840	0.95[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs897842	0.95[CHB][hapmap];0.89[JPT][hapmap];0.81[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2236628	PKHD1L1	Cis_1M	lymphoblastoid	RTeQTL
rs2236628	PKHD1L1	cis	Lymphoblastoid	GTEx
rs2236628	TRHR	cis	parietal	SCAN
rs2236628	SYBU	cis	parietal	SCAN
rs2236628	PKHD1L1	cis	multi-tissue	Pritchard
rs2236628	PKHD1L1	cis	lymphoblastoid	seeQTL

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:110553800-110613000	Weak transcription	NHLF	lung
2	chr8:110583800-110601600	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr8:110586000-110598800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr8:110587800-110605800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr8:110588000-110600600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr8:110588200-110598200	Weak transcription	Ovary	ovary
7	chr8:110588200-110601600	Weak transcription	Left Ventricle	heart
8	chr8:110589200-110598600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr8:110589800-110598200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr8:110589800-110601600	Weak transcription	Right Atrium	heart
11	chr8:110590000-110605600	Weak transcription	K562	blood
12	chr8:110590200-110654800	Weak transcription	Lung	lung
13	chr8:110591200-110601600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr8:110591600-110598400	Weak transcription	Right Ventricle	heart
15	chr8:110591600-110599400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr8:110591600-110601600	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr8:110591600-110609400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr8:110591800-110598200	Weak transcription	Fetal Stomach	stomach
19	chr8:110592000-110601400	Weak transcription	Brain Angular Gyrus	brain
20	chr8:110592200-110601600	Weak transcription	NHEK	skin
21	chr8:110592200-110604600	Weak transcription	Gastric	stomach
22	chr8:110592400-110601800	Weak transcription	Brain Germinal Matrix	brain
23	chr8:110593200-110598600	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr8:110593600-110601400	Weak transcription	HMEC	breast
25	chr8:110594200-110598200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr8:110594600-110598800	Enhancers	Pancreas	Pancrea
27	chr8:110594800-110598400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr8:110594800-110606000	Weak transcription	Fetal Brain Male	brain
29	chr8:110595600-110601600	Weak transcription	Psoas Muscle	Psoas
30	chr8:110596200-110598200	Enhancers	Small Intestine	intestine
31	chr8:110596200-110601600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr8:110596200-110601600	Weak transcription	Fetal Muscle Leg	muscle
33	chr8:110596600-110598400	Strong transcription	Fetal Brain Female	brain
34	chr8:110596600-110599200	Enhancers	Colon Smooth Muscle	Colon
35	chr8:110596800-110608400	Enhancers	Fetal Intestine Large	intestine
36	chr8:110597000-110598200	Enhancers	Rectal Smooth Muscle	rectum
37	chr8:110597000-110598400	Strong transcription	Brain Anterior Caudate	brain
38	chr8:110597000-110598600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr8:110597000-110598600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
40	chr8:110597200-110598400	Genic enhancers	Liver	Liver
41	chr8:110597200-110601000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr8:110597200-110601400	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr8:110597400-110599000	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr8:110597600-110598200	Enhancers	Colonic Mucosa	Colon
45	chr8:110597600-110598200	Genic enhancers	Stomach Smooth Muscle	stomach
46	chr8:110597600-110598400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr8:110597600-110598400	Enhancers	Esophagus	oesophagus
48	chr8:110597600-110598600	Flanking Active TSS	Duodenum Mucosa	Duodenum
49	chr8:110597600-110598600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
50	chr8:110597800-110598200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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