Variant report

Variant	rs2659900
Chromosome Location	chr7:66184443-66184444
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:66092547..66095471-chr7:66182825..66184836,2	K562	blood:
2	chr7:66183509..66185499-chr7:66186909..66189328,2	K562	blood:

Variant related genes	Relation type
ENSG00000243335	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1016265	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10233806	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10244498	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10274883	0.86[AFR][1000 genomes]
rs10950049	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11761542	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs11772819	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs12333370	0.82[AFR][1000 genomes]
rs13226966	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs13242290	0.83[AFR][1000 genomes]
rs13308803	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1544549	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1860469	0.87[AFR][1000 genomes]
rs1860472	0.85[AFR][1000 genomes]
rs1962050	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2003300	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2013908	0.85[AFR][1000 genomes]
rs2109297	0.86[AFR][1000 genomes]
rs2420820	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2659890	0.86[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs2659891	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2659892	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2659893	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2659894	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2659895	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2659896	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2659897	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2659898	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2659901	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2659904	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2659907	0.90[AFR][1000 genomes]
rs2659908	0.90[AFR][1000 genomes]
rs2659914	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2707824	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2707837	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2707839	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2707847	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs28480509	0.86[AFR][1000 genomes]
rs3846973	0.83[AFR][1000 genomes]
rs3857687	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3926380	0.82[AFR][1000 genomes]
rs4506088	0.81[AFR][1000 genomes]
rs4610622	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4717315	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4718383	0.87[AFR][1000 genomes]
rs58347342	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs66981195	0.85[AFR][1000 genomes]
rs6951302	0.87[AFR][1000 genomes]
rs6958200	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6969679	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6975044	0.85[AFR][1000 genomes]
rs6978178	0.86[AFR][1000 genomes]
rs721717	0.87[AFR][1000 genomes]
rs7782587	0.89[AFR][1000 genomes]
rs7792762	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7800620	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7805152	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs881285	0.84[AFR][1000 genomes]
rs974239	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9791712	0.87[AFR][1000 genomes]
rs9791713	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
2	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
3	esv3385090	chr7:66146376-66205022	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	esv3401338	chr7:66147493-66206298	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv888328	chr7:66173040-66327654	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs2659900	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs2659900	GS1-124K5.4	cis	Artery Aorta	GTEx
rs2659900	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs2659900	RNU6-96P	cis	Thyroid	GTEx
rs2659900	RP4-756H11.3	cis	Thyroid	GTEx
rs2659900	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs2659900	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs2659900	RP4-756H11.3	cis	Artery Tibial	GTEx
rs2659900	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs2659900	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs2659900	GTF2IRD1P1	cis	Thyroid	GTEx
rs2659900	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2659900	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs2659900	RP4-756H11.3	cis	Artery Aorta	GTEx
rs2659900	RP4-756H11.3	cis	lung	GTEx
rs2659900	GS1-124K5.4	cis	Stomach	GTEx
rs2659900	GS1-124K5.11	cis	Thyroid	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66148400-66184800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr7:66149000-66199600	Weak transcription	Thymus	Thymus
3	chr7:66149600-66190200	Weak transcription	Hela-S3	cervix
4	chr7:66159600-66190600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr7:66162400-66189400	Weak transcription	Psoas Muscle	Psoas
6	chr7:66162600-66192400	Weak transcription	NH-A	brain
7	chr7:66162600-66196800	Weak transcription	Right Ventricle	heart
8	chr7:66163000-66190800	Weak transcription	Esophagus	oesophagus
9	chr7:66165200-66189800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr7:66165400-66188600	Weak transcription	Lung	lung
11	chr7:66165400-66204600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr7:66165800-66197000	Weak transcription	Right Atrium	heart
13	chr7:66169000-66187400	Weak transcription	Small Intestine	intestine
14	chr7:66173000-66190400	Weak transcription	Fetal Heart	heart
15	chr7:66173200-66190600	Weak transcription	Brain Substantia Nigra	brain
16	chr7:66174200-66184600	Strong transcription	Osteobl	bone
17	chr7:66174200-66190400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr7:66175000-66190800	Weak transcription	Pancreas	Pancrea
19	chr7:66175000-66190800	Weak transcription	Spleen	Spleen
20	chr7:66176400-66204600	Weak transcription	Colonic Mucosa	Colon
21	chr7:66177200-66191200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr7:66177600-66193600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr7:66178000-66186200	Weak transcription	Placenta	Placenta
24	chr7:66178600-66186400	Weak transcription	Aorta	Aorta
25	chr7:66178600-66188400	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr7:66178600-66200400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr7:66178800-66186200	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr7:66178800-66186600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr7:66178800-66190200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr7:66178800-66193600	Weak transcription	Brain Cingulate Gyrus	brain
31	chr7:66178800-66197000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr7:66179000-66189200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr7:66179000-66190000	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr7:66179000-66190600	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr7:66179000-66197200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr7:66179200-66184800	Weak transcription	Primary B cells from peripheral blood	blood
37	chr7:66179200-66186200	Weak transcription	HSMM	muscle
38	chr7:66179200-66188000	Weak transcription	Primary hematopoietic stem cells	blood
39	chr7:66179200-66188200	Weak transcription	Fetal Brain Male	brain
40	chr7:66179200-66189800	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr7:66179200-66190400	Weak transcription	Brain Hippocampus Middle	brain
42	chr7:66179200-66200600	Weak transcription	Duodenum Mucosa	Duodenum
43	chr7:66179400-66185000	Weak transcription	Primary B cells from cord blood	blood
44	chr7:66179400-66187800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr7:66179400-66188200	Weak transcription	Dnd41	blood
46	chr7:66179400-66199800	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr7:66179600-66184600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr7:66179600-66186400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr7:66179600-66188200	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr7:66179600-66204600	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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