Variant report

Variant	rs7129990
Chromosome Location	chr11:73124441-73124442
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:73111818..73115266-chr11:73122319..73124692,3	K562	blood:
2	chr11:73118868..73120938-chr11:73124092..73125726,2	MCF-7	breast:
3	chr11:73124386..73125910-chr11:73135092..73137028,2	K562	blood:
4	chr11:73122593..73125409-chr11:73127410..73129119,2	K562	blood:
5	chr11:73118962..73122327-chr11:73122703..73124989,4	K562	blood:

Extended variants
information (count: 85 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1002126	1.00[CHB][hapmap]
rs1002127	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs10793060	0.81[MKK][hapmap]
rs11235746	1.00[CHB][hapmap]
rs11235770	0.89[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.80[LWK][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11235809	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap]
rs11544310	0.93[EUR][1000 genomes]
rs11544311	0.83[EUR][1000 genomes]
rs11820929	0.82[CHB][hapmap]
rs11821094	0.82[CHB][hapmap]
rs11823913	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11823923	0.82[CHB][hapmap]
rs11824614	0.82[CHB][hapmap]
rs11826896	1.00[CHB][hapmap]
rs11826909	1.00[CHB][hapmap]
rs11828904	0.89[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12275766	0.82[CHB][hapmap]
rs12276892	0.89[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs12277924	0.88[AMR][1000 genomes]
rs12282282	0.82[CHB][hapmap]
rs12285885	0.83[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap]
rs12288753	0.89[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12290623	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12290701	0.82[AMR][1000 genomes]
rs17132115	0.82[AMR][1000 genomes]
rs17244596	0.89[CEU][hapmap]
rs17244602	0.89[CEU][hapmap]
rs17244616	0.89[CEU][hapmap]
rs17310361	0.89[CEU][hapmap]
rs17310374	0.85[CEU][hapmap]
rs17851510	0.89[CEU][hapmap];0.90[GIH][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes]
rs1894076	0.82[CHB][hapmap]
rs1938777	0.94[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2027761	0.82[CHB][hapmap]
rs2027763	0.82[CHB][hapmap]
rs2298469	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2298807	0.82[CHB][hapmap]
rs3741149	0.82[CHB][hapmap]
rs58334887	0.81[EUR][1000 genomes]
rs58573166	0.88[AMR][1000 genomes]
rs60078907	0.80[EUR][1000 genomes]
rs60860405	0.82[AMR][1000 genomes]
rs61345051	0.83[EUR][1000 genomes]
rs6592521	0.82[CHB][hapmap]
rs7101831	1.00[CHB][hapmap]
rs7112924	0.93[EUR][1000 genomes]
rs7114009	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7114376	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs7115055	0.89[CEU][hapmap]
rs7118982	0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7123298	1.00[CHB][hapmap]
rs7123985	0.89[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes]
rs7125598	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7131383	0.82[CHB][hapmap]
rs724111	0.89[CEU][hapmap]
rs725103	0.82[CHB][hapmap]
rs7342205	0.82[CHB][hapmap]
rs73542952	0.83[EUR][1000 genomes]
rs73542960	0.83[EUR][1000 genomes]
rs73542967	0.83[EUR][1000 genomes]
rs73542976	0.83[EUR][1000 genomes]
rs73542979	0.83[EUR][1000 genomes]
rs73542990	0.83[EUR][1000 genomes]
rs73544711	0.81[EUR][1000 genomes]
rs73544716	0.81[EUR][1000 genomes]
rs73544720	0.81[EUR][1000 genomes]
rs7925226	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs7927344	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7930454	0.80[EUR][1000 genomes]
rs7930880	0.82[CHB][hapmap]
rs7934218	0.89[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7935948	0.83[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes]
rs7937066	0.81[ASN][1000 genomes]
rs7938391	0.89[CEU][hapmap];0.94[AMR][1000 genomes]
rs7941359	0.94[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];0.88[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7944099	0.82[CHB][hapmap]
rs7944346	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs7945825	0.86[CEU][hapmap]
rs7951072	0.87[CEU][hapmap]
rs7952686	1.00[CHB][hapmap]
rs876480	0.82[CHB][hapmap]
rs880317	1.00[CHB][hapmap]
rs947837	0.82[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	esv3395161	chr11:73084616-73461577	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv530624	chr11:73114283-73646329	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7129990	CCND1	cis	cerebellum	SCAN
rs7129990	ARHGEF17	cis	multi-tissue	Pritchard
rs7129990	ARHGEF17	cis	Whole Blood	GTEx
rs7129990	HLA-DRB1	trans	brain	seeQTL
rs7129990	P2RY2	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73096200-73130200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:73098600-73126000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr11:73098600-73132400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr11:73099200-73139800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr11:73099200-73141000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr11:73101200-73124800	Weak transcription	Psoas Muscle	Psoas
7	chr11:73113000-73126200	Weak transcription	Small Intestine	intestine
8	chr11:73113400-73125000	Weak transcription	Right Atrium	heart
9	chr11:73113600-73132600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr11:73114600-73125200	Strong transcription	Primary T cells from cord blood	blood
11	chr11:73115200-73126200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr11:73115200-73132200	Weak transcription	Fetal Heart	heart
13	chr11:73115200-73132400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr11:73115200-73149400	Weak transcription	Fetal Kidney	kidney
15	chr11:73116600-73126600	Weak transcription	Stomach Mucosa	stomach
16	chr11:73116800-73132600	Strong transcription	Primary B cells from cord blood	blood
17	chr11:73117000-73131400	Weak transcription	A549	lung
18	chr11:73117800-73130200	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr11:73118800-73128200	Weak transcription	Fetal Brain Male	brain
20	chr11:73118800-73137600	Weak transcription	Colonic Mucosa	Colon
21	chr11:73120200-73127800	Weak transcription	HMEC	breast
22	chr11:73120600-73125200	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr11:73120600-73127400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr11:73120800-73125400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr11:73120800-73126400	Weak transcription	Right Ventricle	heart
26	chr11:73120800-73127800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr11:73120800-73128800	Weak transcription	Fetal Intestine Large	intestine
28	chr11:73120800-73129000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr11:73120800-73129000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr11:73120800-73129200	Weak transcription	Duodenum Mucosa	Duodenum
31	chr11:73120800-73132600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr11:73120800-73133000	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr11:73120800-73133000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr11:73120800-73140600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr11:73120800-73141200	Weak transcription	Esophagus	oesophagus
36	chr11:73120800-73149000	Weak transcription	Fetal Lung	lung
37	chr11:73120800-73149800	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr11:73120800-73150000	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr11:73121000-73124800	Weak transcription	Placenta	Placenta
40	chr11:73121000-73125200	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr11:73121000-73125600	Weak transcription	Adipose Nuclei	Adipose
42	chr11:73121000-73125800	Weak transcription	Primary hematopoietic stem cells	blood
43	chr11:73121000-73126200	Weak transcription	Colon Smooth Muscle	Colon
44	chr11:73121000-73129000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr11:73121000-73133000	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr11:73121000-73150200	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr11:73121200-73129000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr11:73121600-73132400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr11:73121800-73125800	Weak transcription	GM12878-XiMat	blood
50	chr11:73121800-73128200	Enhancers	Brain Cingulate Gyrus	brain

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