Variant report

Variant	rs2342765
Chromosome Location	chr6:150180009-150180010
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:150179997-150180935	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:150179152..150182085-chr6:150183567..150186246,3	K562	blood:
2	chr6:150166110..150169897-chr6:150177295..150181208,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000268592	TF binding region
ENSG00000120256	Chromatin interaction
ENSG00000268592	Chromatin interaction

Extended variants
information (count: 191 )
Associated
traits (count: 23 )

rSNPs within LD-proxies of this variant (count:189)

rs_ID	r²[population]
rs10214845	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[EUR][1000 genomes]
rs10452626	0.83[EUR][1000 genomes]
rs10457850	0.83[EUR][1000 genomes]
rs10457851	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[EUR][1000 genomes]
rs10747276	0.95[CEU][hapmap]
rs10782316	0.95[CEU][hapmap];0.89[TSI][hapmap]
rs10782317	0.95[CEU][hapmap];0.89[TSI][hapmap]
rs10782318	0.95[CEU][hapmap];0.89[TSI][hapmap]
rs10872646	0.95[CEU][hapmap];0.89[TSI][hapmap]
rs10872647	0.91[CEU][hapmap]
rs10872650	0.95[CEU][hapmap]
rs10872651	0.81[EUR][1000 genomes]
rs10872652	0.83[EUR][1000 genomes]
rs10872653	0.82[EUR][1000 genomes]
rs10872656	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs1108889	0.95[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1112729	0.83[EUR][1000 genomes]
rs1112730	1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs11155674	0.95[CEU][hapmap];0.86[TSI][hapmap]
rs11155683	0.83[EUR][1000 genomes]
rs11155685	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs11155689	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[EUR][1000 genomes]
rs11968921	0.85[EUR][1000 genomes]
rs12174349	0.95[CEU][hapmap]
rs12175575	0.82[EUR][1000 genomes]
rs12176034	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs12179031	0.83[EUR][1000 genomes]
rs12182220	0.86[EUR][1000 genomes]
rs12195866	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[TSI][hapmap]
rs12210605	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs12213779	0.83[EUR][1000 genomes]
rs12525871	0.83[EUR][1000 genomes]
rs12526675	0.95[CEU][hapmap];0.86[TSI][hapmap]
rs12528279	0.95[CEU][hapmap];0.89[TSI][hapmap]
rs12660304	0.95[CEU][hapmap];0.86[TSI][hapmap]
rs13215691	0.86[EUR][1000 genomes]
rs1413654	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[EUR][1000 genomes]
rs1413655	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[EUR][1000 genomes]
rs1572229	0.95[CEU][hapmap]
rs17672976	0.83[EUR][1000 genomes]
rs17673294	0.88[EUR][1000 genomes]
rs1889473	0.89[EUR][1000 genomes]
rs1934534	0.95[CEU][hapmap];0.86[TSI][hapmap]
rs1984111	0.89[EUR][1000 genomes]
rs2065663	0.95[CEU][hapmap];0.85[CHB][hapmap]
rs2065664	1.00[CEU][hapmap];0.91[TSI][hapmap]
rs2095375	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[EUR][1000 genomes]
rs2151912	0.89[EUR][1000 genomes]
rs2151913	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs2184369	0.84[EUR][1000 genomes]
rs2184370	0.86[EUR][1000 genomes]
rs2185352	1.00[CEU][hapmap];0.86[TSI][hapmap]
rs2210683	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2275045	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs2275046	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs2297930	0.95[CEU][hapmap];0.86[TSI][hapmap]
rs2342764	0.95[CEU][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs2342857	0.88[EUR][1000 genomes]
rs2342858	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[EUR][1000 genomes]
rs2342860	0.84[EUR][1000 genomes]
rs2342861	0.84[EUR][1000 genomes]
rs2880435	0.83[EUR][1000 genomes]
rs2880436	0.95[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35031906	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[TSI][hapmap]
rs3763162	1.00[CEU][hapmap];0.86[CHB][hapmap];0.80[CHD][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs3763163	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs3798761	0.95[CEU][hapmap];0.86[TSI][hapmap]
rs3805748	0.82[EUR][1000 genomes]
rs3805749	0.95[CEU][hapmap]
rs3805750	0.86[EUR][1000 genomes]
rs3805751	0.86[EUR][1000 genomes]
rs3805752	0.84[EUR][1000 genomes]
rs3805753	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[EUR][1000 genomes]
rs3828700	0.86[EUR][1000 genomes]
rs3924871	0.95[CEU][hapmap];0.86[TSI][hapmap]
rs4242279	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs4354168	0.91[CEU][hapmap];0.82[TSI][hapmap]
rs4455682	0.86[TSI][hapmap]
rs4552	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[EUR][1000 genomes]
rs4642491	0.82[EUR][1000 genomes]
rs4816	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs4869730	0.88[EUR][1000 genomes]
rs4869731	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[EUR][1000 genomes]
rs4869750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4869966	0.83[EUR][1000 genomes]
rs4870015	0.87[EUR][1000 genomes]
rs4870019	0.88[EUR][1000 genomes]
rs4870020	0.87[EUR][1000 genomes]
rs4870048	0.89[EUR][1000 genomes]
rs4870049	0.86[EUR][1000 genomes]
rs4870050	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs4870052	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs4870054	0.91[CEU][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs4870055	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4870509	0.95[CEU][hapmap]
rs4870529	0.81[CEU][hapmap]
rs55763431	0.84[EUR][1000 genomes]
rs56103941	0.86[EUR][1000 genomes]
rs56374774	0.84[EUR][1000 genomes]
rs62441303	0.83[EUR][1000 genomes]
rs62441335	0.86[EUR][1000 genomes]
rs6420132	0.89[EUR][1000 genomes]
rs6899661	0.88[EUR][1000 genomes]
rs6903998	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs6913486	0.95[CEU][hapmap];0.86[TSI][hapmap]
rs6914319	0.88[EUR][1000 genomes]
rs6936395	0.88[EUR][1000 genomes]
rs7450246	0.95[CEU][hapmap];0.86[TSI][hapmap]
rs7738696	0.95[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7740784	0.86[EUR][1000 genomes]
rs7743823	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7744015	0.84[EUR][1000 genomes]
rs7744105	0.95[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.87[JPT][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7745915	0.89[EUR][1000 genomes]
rs7752089	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs7753812	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[TSI][hapmap]
rs7764846	0.89[EUR][1000 genomes]
rs7767622	0.95[CEU][hapmap];0.86[TSI][hapmap]
rs7769115	0.95[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.87[JPT][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7818	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs868375	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs880245	0.95[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.87[JPT][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs880246	0.94[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9285524	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[TSI][hapmap]
rs9285525	0.87[EUR][1000 genomes]
rs9322209	0.95[CEU][hapmap];0.86[TSI][hapmap]
rs9322214	0.95[CEU][hapmap];0.86[TSI][hapmap]
rs9322218	0.95[CEU][hapmap];0.89[CHB][hapmap];0.83[EUR][1000 genomes]
rs9322219	0.95[CEU][hapmap];0.86[CHB][hapmap];0.84[EUR][1000 genomes]
rs9322220	0.83[EUR][1000 genomes]
rs9322221	0.82[EUR][1000 genomes]
rs9322223	0.87[EUR][1000 genomes]
rs9322224	0.89[EUR][1000 genomes]
rs933055	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[EUR][1000 genomes]
rs9371199	0.86[EUR][1000 genomes]
rs9371201	0.91[CEU][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs9371207	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9371486	0.82[EUR][1000 genomes]
rs9372044	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[EUR][1000 genomes]
rs9383546	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[EUR][1000 genomes]
rs9383843	0.82[EUR][1000 genomes]
rs9383864	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9383865	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9383874	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9393175	0.95[CEU][hapmap];0.86[TSI][hapmap]
rs9397022	0.88[EUR][1000 genomes]
rs9397036	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9397357	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[EUR][1000 genomes]
rs9478291	0.95[CEU][hapmap];0.84[TSI][hapmap]
rs9478848	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs9479094	0.95[CEU][hapmap];0.84[TSI][hapmap]
rs9479808	0.95[CEU][hapmap]
rs9479810	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[TSI][hapmap]
rs9505972	0.81[EUR][1000 genomes]
rs9505974	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[EUR][1000 genomes]
rs9505975	0.80[EUR][1000 genomes]
rs952165	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[EUR][1000 genomes]
rs952166	0.87[EUR][1000 genomes]
rs958953	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs9688350	0.95[CEU][hapmap]
rs9688412	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs9688699	0.95[CEU][hapmap]
rs9688803	0.85[EUR][1000 genomes]
rs9688809	0.86[EUR][1000 genomes]
rs9688867	0.82[EUR][1000 genomes]
rs9688897	0.85[EUR][1000 genomes]
rs9688902	0.85[EUR][1000 genomes]
rs9688938	0.86[EUR][1000 genomes]
rs9688940	0.86[EUR][1000 genomes]
rs9689025	0.85[EUR][1000 genomes]
rs9689036	1.00[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs9689242	0.86[EUR][1000 genomes]
rs9689269	0.95[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs9689447	0.87[EUR][1000 genomes]
rs9689694	0.81[EUR][1000 genomes]
rs9765929	0.83[EUR][1000 genomes]
rs9765965	0.82[EUR][1000 genomes]
rs9766004	0.95[CEU][hapmap];0.89[TSI][hapmap]
rs9766214	0.82[EUR][1000 genomes]
rs9766444	0.82[EUR][1000 genomes]
rs9766525	0.83[EUR][1000 genomes]
rs9766562	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[EUR][1000 genomes]
rs9767077	0.85[EUR][1000 genomes]
rs9767105	0.95[CEU][hapmap];0.86[TSI][hapmap]
rs9767122	1.00[CEU][hapmap];0.83[CHB][hapmap];0.80[JPT][hapmap];0.83[EUR][1000 genomes]
rs9767123	0.95[CEU][hapmap];0.86[TSI][hapmap]
rs9767309	0.95[CEU][hapmap];0.86[TSI][hapmap]
rs9800736	0.95[CEU][hapmap];0.86[TSI][hapmap]
rs9800806	0.95[CEU][hapmap];0.86[TSI][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	nsv886764	chr6:150114745-150393683	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv517022	chr6:150145001-150426272	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:23)

SNP	Gene	Cis/trans	Tissue	Source
rs2342765	LATS1	cis	parietal	SCAN
rs2342765	LATS1	cis	cerebellum	SCAN
rs2342765	RP11-350J20.9	cis	Esophagus Mucosa	GTEx
rs2342765	GINM1	cis	Nerve Tibial	GTEx
rs2342765	RP11-350J20.5	cis	Thyroid	GTEx
rs2342765	PPIL4	cis	parietal	SCAN
rs2342765	NUP43	cis	multi-tissue	Pritchard
rs2342765	PPIL4	cis	cerebellum	SCAN
rs2342765	LRP11	cis	Skin Sun Exposed Lower leg	GTEx
rs2342765	NUP43	cis	Whole Blood	GTEx
rs2342765	RP11-350J20.5	cis	Adipose Subcutaneous	GTEx
rs2342765	RP11-350J20.5	cis	Nerve Tibial	GTEx
rs2342765	RP11-350J20.5	cis	Esophagus Mucosa	GTEx
rs2342765	RMND1	cis	cerebellum	SCAN
rs2342765	RP11-350J20.9	cis	Skin Sun Exposed Lower leg	GTEx
rs2342765	GINM1	cis	Whole Blood	GTEx
rs2342765	RP11-350J20.5	cis	Esophagus Muscularis	GTEx
rs2342765	LRP11	cis	parietal	SCAN
rs2342765	PCMT1	cis	multi-tissue	Pritchard
rs2342765	LRP11	cis	cerebellum	SCAN
rs2342765	RP11-350J20.5	cis	Skin Sun Exposed Lower leg	GTEx
rs2342765	RP11-350J20.5	cis	lung	GTEx
rs2342765	RP11-350J20.5	cis	Artery Tibial	GTEx

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150073800-150182400	Weak transcription	Fetal Brain Male	brain
2	chr6:150155800-150182600	Weak transcription	Dnd41	blood
3	chr6:150164400-150181800	Weak transcription	Brain Germinal Matrix	brain
4	chr6:150165000-150181800	Weak transcription	Fetal Brain Female	brain
5	chr6:150167800-150181400	Weak transcription	Right Atrium	heart
6	chr6:150168800-150182600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr6:150168800-150183400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr6:150169000-150181200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:150169200-150183000	Weak transcription	Brain Substantia Nigra	brain
10	chr6:150169400-150183200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr6:150172600-150181600	Weak transcription	Brain Angular Gyrus	brain
12	chr6:150173000-150181200	Weak transcription	Liver	Liver
13	chr6:150173000-150181600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr6:150173000-150184200	Weak transcription	Aorta	Aorta
15	chr6:150173200-150183200	Weak transcription	Ovary	ovary
16	chr6:150173800-150181800	Weak transcription	Brain Hippocampus Middle	brain
17	chr6:150174000-150181600	Weak transcription	Brain Anterior Caudate	brain
18	chr6:150174200-150181600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr6:150174200-150181600	Weak transcription	Fetal Stomach	stomach
20	chr6:150174200-150181800	Weak transcription	Adipose Nuclei	Adipose
21	chr6:150174200-150182600	Weak transcription	Fetal Muscle Trunk	muscle
22	chr6:150176000-150181800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr6:150176200-150181200	Weak transcription	Esophagus	oesophagus
24	chr6:150176200-150183200	Weak transcription	Fetal Intestine Large	intestine
25	chr6:150176400-150182000	Weak transcription	Stomach Smooth Muscle	stomach
26	chr6:150176600-150180600	Weak transcription	Gastric	stomach
27	chr6:150176600-150181400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr6:150176600-150182400	Weak transcription	Fetal Intestine Small	intestine
29	chr6:150176600-150183200	Weak transcription	Colon Smooth Muscle	Colon
30	chr6:150176600-150183400	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr6:150176800-150180600	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr6:150176800-150181200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr6:150176800-150181400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr6:150176800-150181600	Weak transcription	Lung	lung
35	chr6:150176800-150182200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr6:150176800-150183400	Weak transcription	HSMMtube	muscle
37	chr6:150177200-150180200	Weak transcription	Stomach Mucosa	stomach
38	chr6:150177200-150180800	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr6:150177200-150181200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr6:150177200-150181200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr6:150177200-150181200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr6:150177200-150182000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr6:150177200-150183000	Weak transcription	Fetal Kidney	kidney
44	chr6:150177600-150180800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr6:150177600-150183000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr6:150177600-150183200	Weak transcription	Fetal Lung	lung
47	chr6:150178000-150180600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr6:150178000-150183200	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr6:150178000-150183200	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr6:150178200-150181200	Weak transcription	Brain Inferior Temporal Lobe	brain

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