Variant report

Variant	rs9399689
Chromosome Location	chr6:149830661-149830662
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:149830636..149832927-chr6:149835174..149836889,2	K562	blood:
2	chr6:149829549..149832059-chr6:149838355..149841591,3	K562	blood:
3	chr6:149827201..149829312-chr6:149829316..149833197,3	K562	blood:
4	chr6:149818918..149821487-chr6:149828653..149831549,2	K562	blood:

Variant related genes	Relation type
ENSG00000131013	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10485097	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10782310	0.81[CHB][hapmap]
rs10782312	0.81[CHB][hapmap]
rs11155662	0.81[CHB][hapmap]
rs11155670	0.81[CHB][hapmap]
rs11155671	0.81[CHB][hapmap]
rs1125107	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12234128	0.81[CHB][hapmap]
rs12524946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12529698	0.81[CHB][hapmap]
rs12663698	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12665533	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1474640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17732745	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2064520	0.81[CHB][hapmap]
rs2105200	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2341550	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2341551	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2341768	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28580659	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2880075	0.93[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34870994	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3734295	0.81[CHB][hapmap]
rs3777949	0.81[CHB][hapmap]
rs3798761	0.81[CHB][hapmap]
rs3813675	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3924871	0.81[CHB][hapmap]
rs4869797	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4870509	0.81[CHB][hapmap]
rs4897128	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4897130	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4897131	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4897132	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4897133	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4897137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4897138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4897139	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60404985	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62439778	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62442787	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62442788	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62442789	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62442790	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62442792	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62442793	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62442795	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62442798	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6570968	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6911016	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6913486	0.81[CHB][hapmap]
rs6929614	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7450246	0.81[CHB][hapmap]
rs761617	1.00[CHD][hapmap];0.88[JPT][hapmap];0.84[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7740278	0.81[CHB][hapmap]
rs7753560	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7767622	0.81[CHB][hapmap]
rs7774559	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7774597	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs909792	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9285521	0.81[CHB][hapmap]
rs9322184	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9322185	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9322188	0.80[CHB][hapmap]
rs9322198	0.81[CHB][hapmap]
rs9322200	0.80[CHB][hapmap]
rs9322209	0.81[CHB][hapmap]
rs9322214	0.81[CHB][hapmap]
rs9373594	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9373595	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9373596	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9377220	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9377221	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9377223	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9377224	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9377230	0.81[CHB][hapmap]
rs9390684	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9390687	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9390688	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9390689	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9393175	0.80[CHB][hapmap]
rs9399690	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9404042	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9404043	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9404044	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9404048	0.81[CHB][hapmap]
rs9406344	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9498368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9689569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9689723	0.81[CHB][hapmap]
rs9718079	0.81[CHB][hapmap]
rs9767105	0.81[CHB][hapmap]
rs9767123	0.81[CHB][hapmap]
rs9767555	0.81[CHB][hapmap]
rs9767713	0.81[CHB][hapmap]
rs9800580	0.81[CHB][hapmap]
rs9800614	0.81[CHB][hapmap]
rs9800648	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9800686	0.81[CHB][hapmap]
rs9800736	0.81[CHB][hapmap]
rs9968911	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530444	chr6:149654540-149848997	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv1832313	chr6:149789511-149840750	Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs9399689	PPIL4	cis	cerebellum	SCAN
rs9399689	LRP11	cis	parietal	SCAN
rs9399689	LATS1	cis	cerebellum	SCAN
rs9399689	LRP11	cis	cerebellum	SCAN
rs9399689	RP11-350J20.5	cis	Skin Sun Exposed Lower leg	GTEx
rs9399689	PPIL4	cis	parietal	SCAN
rs9399689	LATS1	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149806400-149832000	Weak transcription	HSMMtube	muscle
2	chr6:149806400-149844800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr6:149806800-149832400	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr6:149807000-149832200	Weak transcription	Lung	lung
5	chr6:149807000-149849000	Weak transcription	Gastric	stomach
6	chr6:149807200-149832000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr6:149807200-149835000	Weak transcription	Spleen	Spleen
8	chr6:149807200-149842600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr6:149810800-149851600	Weak transcription	Esophagus	oesophagus
10	chr6:149811200-149860600	Weak transcription	Aorta	Aorta
11	chr6:149815600-149845000	Weak transcription	Small Intestine	intestine
12	chr6:149817000-149830800	Weak transcription	Brain Angular Gyrus	brain
13	chr6:149818400-149843800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:149818800-149845000	Weak transcription	A549	lung
15	chr6:149819200-149832000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr6:149820400-149831000	Weak transcription	Ovary	ovary
17	chr6:149820400-149831600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr6:149820400-149832000	Weak transcription	Fetal Heart	heart
19	chr6:149820400-149837400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr6:149820400-149840800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr6:149820400-149845200	Weak transcription	Hela-S3	cervix
22	chr6:149820400-149849000	Weak transcription	Psoas Muscle	Psoas
23	chr6:149820400-149850200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr6:149820600-149831600	Weak transcription	Fetal Stomach	stomach
25	chr6:149820600-149832400	Weak transcription	Fetal Muscle Trunk	muscle
26	chr6:149820600-149832400	Weak transcription	Dnd41	blood
27	chr6:149820600-149835000	Weak transcription	NHEK	skin
28	chr6:149820600-149838400	Weak transcription	Rectal Smooth Muscle	rectum
29	chr6:149820600-149839400	Weak transcription	Thymus	Thymus
30	chr6:149820600-149842600	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr6:149820600-149847800	Weak transcription	Brain Substantia Nigra	brain
32	chr6:149820600-149851400	Weak transcription	NHLF	lung
33	chr6:149820600-149865200	Weak transcription	Stomach Mucosa	stomach
34	chr6:149820800-149832600	Weak transcription	HUVEC	blood vessel
35	chr6:149820800-149841800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr6:149820800-149848200	Weak transcription	Pancreas	Pancrea
37	chr6:149821200-149835200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr6:149821200-149835200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr6:149821400-149839800	Weak transcription	HMEC	breast
40	chr6:149821600-149835200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr6:149821600-149837400	Weak transcription	Fetal Kidney	kidney
42	chr6:149822600-149845000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr6:149823400-149839200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr6:149823600-149832200	Weak transcription	Fetal Brain Female	brain
45	chr6:149823800-149851800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr6:149824200-149834000	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr6:149824200-149842600	Weak transcription	Brain Germinal Matrix	brain
48	chr6:149824200-149846000	Weak transcription	Fetal Brain Male	brain
49	chr6:149824400-149832200	Weak transcription	Colon Smooth Muscle	Colon
50	chr6:149824400-149862200	Strong transcription	Liver	Liver

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