Variant report

Variant	rs2659892
Chromosome Location	chr7:66200305-66200306
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:66198882..66202892-chr7:66203782..66206309,4	K562	blood:
2	chr7:66199744..66203174-chr7:66203641..66207564,4	MCF-7	breast:
3	chr7:66198882..66201423-chr7:66203889..66205689,3	K562	blood:
4	chr7:66194758..66197486-chr7:66199792..66202230,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000243335	Chromatin interaction
ENSG00000272831	Chromatin interaction
ENSG00000154710	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 20 )

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

rs_ID	r²[population]
rs10107	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs1016265	0.82[AMR][1000 genomes]
rs10233806	0.84[CEU][hapmap];0.87[AFR][1000 genomes]
rs10244498	0.83[CEU][hapmap];0.87[AFR][1000 genomes]
rs10265311	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs10271548	0.82[EUR][1000 genomes]
rs10274883	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10278014	0.95[CEU][hapmap];0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10950043	0.83[EUR][1000 genomes]
rs10950046	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10950049	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10950050	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11761542	0.96[CEU][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11772819	0.96[CEU][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11772884	0.81[EUR][1000 genomes]
rs12333370	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12673450	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs13226170	0.84[EUR][1000 genomes]
rs13226966	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13232191	0.83[EUR][1000 genomes]
rs13240501	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs13242290	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13308803	0.95[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13536	0.95[CEU][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes]
rs1544549	0.85[AFR][1000 genomes]
rs17747530	0.82[EUR][1000 genomes]
rs1860469	0.96[CEU][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1860472	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1962050	0.83[CEU][hapmap]
rs1968126	0.87[EUR][1000 genomes]
rs2003300	0.92[AFR][1000 genomes]
rs2013908	0.96[CEU][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2024192	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2109295	0.82[EUR][1000 genomes]
rs2109297	0.95[CEU][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2420610	0.83[EUR][1000 genomes]
rs2420611	0.84[EUR][1000 genomes]
rs2420820	0.85[AFR][1000 genomes]
rs2420821	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2659890	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2659891	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2659893	0.96[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2659894	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2659895	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2659896	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2659897	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2659898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2659900	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2659901	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2659904	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2659907	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2659908	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2659914	0.85[AFR][1000 genomes]
rs2707824	0.96[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2707837	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2707839	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2707847	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28431318	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28480509	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28731376	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs35378740	0.83[EUR][1000 genomes]
rs3846973	0.95[CEU][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3926380	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4506088	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4610622	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4717315	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4718377	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4718383	0.96[CEU][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58347342	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61348003	0.84[EUR][1000 genomes]
rs6460307	0.95[CEU][hapmap]
rs66981195	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6951302	1.00[CEU][hapmap];0.85[JPT][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6951946	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6955837	0.96[CEU][hapmap];0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6969679	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6971059	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6973249	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6975044	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6978178	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs721717	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7384021	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7385102	0.87[EUR][1000 genomes]
rs7782587	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7793723	0.85[EUR][1000 genomes]
rs7800620	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7805152	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7808013	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs801194	0.90[EUR][1000 genomes]
rs801195	0.95[CEU][hapmap];0.80[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs801202	0.88[EUR][1000 genomes]
rs801203	0.88[EUR][1000 genomes]
rs801204	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs801206	0.88[EUR][1000 genomes]
rs801208	0.88[EUR][1000 genomes]
rs801209	0.88[EUR][1000 genomes]
rs881285	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs974239	0.83[CEU][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9791712	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9791713	0.95[CEU][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv971490	chr7:66192193-66212423	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs2659892	GS1-124K5.2	cis	Whole Blood	GTEx
rs2659892	GS1-124K5.4	cis	Skin Sun Exposed Lower leg	GTEx
rs2659892	GTF2IRD1P1	cis	Thyroid	GTEx
rs2659892	LINC00174	cis	Thyroid	GTEx
rs2659892	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs2659892	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs2659892	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs2659892	RP4-756H11.3	cis	Artery Tibial	GTEx
rs2659892	RP4-756H11.3	cis	Artery Aorta	GTEx
rs2659892	GS1-124K5.4	cis	Stomach	GTEx
rs2659892	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs2659892	GS1-124K5.4	cis	Artery Aorta	GTEx
rs2659892	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs2659892	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2659892	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs2659892	RP4-756H11.3	cis	lung	GTEx
rs2659892	GS1-124K5.11	cis	Thyroid	GTEx
rs2659892	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs2659892	RNU6-96P	cis	Thyroid	GTEx
rs2659892	RP4-756H11.3	cis	Thyroid	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66165400-66204600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr7:66176400-66204600	Weak transcription	Colonic Mucosa	Colon
3	chr7:66178600-66200400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr7:66179200-66200600	Weak transcription	Duodenum Mucosa	Duodenum
5	chr7:66179600-66204600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr7:66181600-66202000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr7:66182800-66205000	Weak transcription	Gastric	stomach
8	chr7:66188400-66201800	Weak transcription	Fetal Brain Male	brain
9	chr7:66190000-66200400	Weak transcription	HepG2	liver
10	chr7:66190000-66201200	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr7:66190400-66204600	Weak transcription	Stomach Mucosa	stomach
12	chr7:66190600-66201200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr7:66190800-66200400	Weak transcription	Primary hematopoietic stem cells	blood
14	chr7:66190800-66200600	Weak transcription	HSMM	muscle
15	chr7:66190800-66204400	Weak transcription	Fetal Heart	heart
16	chr7:66190800-66204600	Weak transcription	NHEK	skin
17	chr7:66191000-66200400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr7:66191000-66200600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr7:66191000-66200600	Weak transcription	Brain Angular Gyrus	brain
20	chr7:66191200-66200400	Weak transcription	Aorta	Aorta
21	chr7:66191200-66200400	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr7:66191200-66200400	Weak transcription	Dnd41	blood
23	chr7:66191200-66204600	Weak transcription	NHLF	lung
24	chr7:66191200-66205000	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr7:66191400-66200600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr7:66191400-66204600	Weak transcription	Primary T cells from cord blood	blood
27	chr7:66191600-66204600	Weak transcription	NHDF-Ad	bronchial
28	chr7:66191800-66204800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr7:66193800-66200400	Weak transcription	Fetal Lung	lung
30	chr7:66193800-66200800	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr7:66193800-66204800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr7:66194000-66200400	Weak transcription	Colon Smooth Muscle	Colon
33	chr7:66194000-66200800	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr7:66194000-66204800	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr7:66194000-66205000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr7:66194000-66205000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr7:66194600-66204600	Weak transcription	Fetal Kidney	kidney
38	chr7:66194600-66205000	Weak transcription	Spleen	Spleen
39	chr7:66195200-66200400	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr7:66195400-66200400	Weak transcription	Stomach Smooth Muscle	stomach
41	chr7:66195600-66200400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr7:66195600-66200400	Weak transcription	Fetal Brain Female	brain
43	chr7:66195600-66200600	Weak transcription	Brain Germinal Matrix	brain
44	chr7:66195600-66204800	Weak transcription	Lung	lung
45	chr7:66196200-66200800	Weak transcription	Fetal Intestine Large	intestine
46	chr7:66197000-66204600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr7:66197200-66200400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr7:66197200-66200400	Weak transcription	Fetal Intestine Small	intestine
49	chr7:66197200-66200600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr7:66197200-66200600	Weak transcription	Adipose Nuclei	Adipose

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