Variant report

Variant	rs974239
Chromosome Location	chr7:66213491-66213492
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:66117314..66120062-chr7:66210977..66213938,2	K562	blood:
2	chr7:66203955..66208659-chr7:66209716..66215353,8	K562	blood:
3	chr7:66145930..66148922-chr7:66213233..66215140,2	MCF-7	breast:
4	chr7:66211368..66213994-chr7:66217034..66219333,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000243335	Chromatin interaction
ENSG00000272831	Chromatin interaction
ENSG00000154710	Chromatin interaction
ENSG00000226824	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 24 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10107	0.89[CEU][hapmap];0.83[CHB][hapmap];0.94[YRI][hapmap]
rs1016265	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10233806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10244498	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10274883	0.84[AFR][1000 genomes]
rs10278014	0.88[CEU][hapmap];0.83[CHB][hapmap];0.87[GIH][hapmap];0.92[LWK][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.94[YRI][hapmap]
rs10281499	0.83[CHB][hapmap];0.94[YRI][hapmap]
rs10950049	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10950050	0.81[AFR][1000 genomes]
rs11761542	0.88[CEU][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11772819	0.92[CEU][hapmap];0.86[CHB][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13226966	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13242290	0.81[AFR][1000 genomes]
rs13308803	0.87[CEU][hapmap];0.86[CHB][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs13536	0.89[CEU][hapmap];0.83[CHB][hapmap];0.87[GIH][hapmap];0.92[LWK][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.94[YRI][hapmap]
rs1544549	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1860469	0.92[CEU][hapmap];0.83[CHB][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes]
rs1860472	0.83[AFR][1000 genomes]
rs1962050	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2003300	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2013908	0.89[CEU][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes]
rs2109297	0.89[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.92[LWK][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes]
rs2420820	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2659890	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2659891	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2659892	0.83[CEU][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2659893	0.88[CEU][hapmap];0.83[CHB][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2659894	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2659895	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2659896	0.82[AMR][1000 genomes]
rs2659897	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2659898	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2659900	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2659901	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2659904	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2659907	0.87[AFR][1000 genomes]
rs2659908	0.87[AFR][1000 genomes]
rs2659914	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2707824	0.89[CEU][hapmap];0.83[CHB][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2707837	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2707839	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2707847	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs28480509	0.84[AFR][1000 genomes]
rs3764903	0.80[MKK][hapmap]
rs3846973	0.89[CEU][hapmap];0.83[CHB][hapmap];0.89[GIH][hapmap];0.92[LWK][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes]
rs3857687	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4610622	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4717315	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4718383	0.89[CEU][hapmap];0.83[CHB][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes]
rs58347342	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6460307	0.89[CEU][hapmap];0.87[GIH][hapmap];0.92[LWK][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.94[YRI][hapmap]
rs66981195	0.83[AFR][1000 genomes]
rs6951302	0.86[CEU][hapmap];0.80[CHB][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes]
rs6955837	0.89[CEU][hapmap];0.83[CHB][hapmap];0.94[YRI][hapmap]
rs6958200	0.89[EUR][1000 genomes]
rs6969679	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6975044	0.87[AFR][1000 genomes]
rs6978178	0.84[AFR][1000 genomes]
rs721717	0.85[AFR][1000 genomes]
rs7782587	0.84[AFR][1000 genomes]
rs7792762	0.85[EUR][1000 genomes]
rs7800620	0.86[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.92[LWK][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7805152	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs801195	0.89[CEU][hapmap];0.83[CHB][hapmap];0.87[GIH][hapmap];0.89[LWK][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap]
rs801204	0.92[CEU][hapmap];0.83[CHB][hapmap];0.93[YRI][hapmap]
rs881285	0.82[AFR][1000 genomes]
rs9791712	0.85[AFR][1000 genomes]
rs9791713	0.89[CEU][hapmap];0.83[CHB][hapmap];0.85[GIH][hapmap];0.92[LWK][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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:24)

SNP	Gene	Cis/trans	Tissue	Source
rs974239	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs974239	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs974239	SBDS	cis	cerebellum	SCAN
rs974239	GS1-124K5.4	cis	Artery Aorta	GTEx
rs974239	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs974239	CRCP	cis	parietal	SCAN
rs974239	GS1-124K5.4	cis	Stomach	GTEx
rs974239	RP4-756H11.3	cis	Artery Tibial	GTEx
rs974239	GUSB	cis	parietal	SCAN
rs974239	RP4-756H11.3	cis	lung	GTEx
rs974239	CRCP	cis	cerebellum	SCAN
rs974239	RNU6-96P	cis	Thyroid	GTEx
rs974239	RP4-756H11.3	cis	Artery Aorta	GTEx
rs974239	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs974239	GUSB	cis	cerebellum	SCAN
rs974239	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs974239	RP4-756H11.3	cis	Thyroid	GTEx
rs974239	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs974239	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs974239	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs974239	GTF2IRD1P1	cis	Thyroid	GTEx
rs974239	RABGEF1	cis	cerebellum	SCAN
rs974239	TPST1	cis	lymphoblastoid	seeQTL
rs974239	GS1-124K5.11	cis	Thyroid	GTEx

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66206400-66216600	Weak transcription	Spleen	Spleen
2	chr7:66206800-66213600	Weak transcription	Small Intestine	intestine
3	chr7:66206800-66216400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr7:66206800-66223400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr7:66206800-66232600	Weak transcription	Primary T cells from cord blood	blood
6	chr7:66206800-66238800	Weak transcription	Aorta	Aorta
7	chr7:66207000-66213800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr7:66207000-66213800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr7:66207000-66216200	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr7:66207000-66216400	Weak transcription	Right Atrium	heart
11	chr7:66207000-66216600	Weak transcription	Esophagus	oesophagus
12	chr7:66207000-66222200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr7:66207000-66227400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr7:66207000-66227400	Weak transcription	Fetal Stomach	stomach
15	chr7:66207000-66230600	Weak transcription	Fetal Intestine Large	intestine
16	chr7:66207000-66230600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr7:66207000-66234000	Weak transcription	Fetal Thymus	thymus
18	chr7:66207000-66238400	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr7:66207000-66238400	Weak transcription	Fetal Muscle Trunk	muscle
20	chr7:66207000-66255200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr7:66207200-66213600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr7:66207200-66223400	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr7:66207600-66213600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr7:66207600-66213800	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr7:66207600-66214000	Weak transcription	Gastric	stomach
26	chr7:66207600-66220400	Weak transcription	Brain Angular Gyrus	brain
27	chr7:66207600-66220400	Weak transcription	Brain Substantia Nigra	brain
28	chr7:66207600-66223200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr7:66207600-66223400	Weak transcription	K562	blood
30	chr7:66207600-66239800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr7:66207800-66219800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr7:66207800-66220600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr7:66207800-66225800	Weak transcription	Fetal Muscle Leg	muscle
34	chr7:66208000-66213800	Weak transcription	Placenta	Placenta
35	chr7:66208000-66215800	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr7:66208000-66216400	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr7:66208000-66217800	Weak transcription	Right Ventricle	heart
38	chr7:66208000-66219400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr7:66208000-66230600	Weak transcription	Duodenum Mucosa	Duodenum
40	chr7:66208000-66232400	Weak transcription	Thymus	Thymus
41	chr7:66208000-66236800	Weak transcription	Dnd41	blood
42	chr7:66208000-66238000	Weak transcription	A549	lung
43	chr7:66208000-66238600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr7:66208000-66238600	Weak transcription	Brain Germinal Matrix	brain
45	chr7:66208000-66240800	Weak transcription	HSMMtube	muscle
46	chr7:66208000-66241800	Weak transcription	Hela-S3	cervix
47	chr7:66208200-66213800	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr7:66208400-66219400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr7:66208800-66214000	Weak transcription	Left Ventricle	heart
50	chr7:66208800-66216400	Weak transcription	Pancreas	Pancrea

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