Variant report

Variant	rs7945972
Chromosome Location	chr11:63477279-63477280
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:63466075..63469317-chr11:63473258..63477515,3	MCF-7	breast:
2	chr11:63476721..63479667-chr11:63483897..63486207,2	K562	blood:
3	chr11:63470955..63472959-chr11:63475975..63477902,3	K562	blood:
4	chr11:63475402..63478468-chr11:63484707..63487659,3	K562	blood:
5	chr11:63477261..63480849-chr11:63481201..63484303,3	K562	blood:
6	chr11:63471459..63475657-chr11:63475722..63478303,6	K562	blood:

Variant related genes	Relation type
ENSG00000271100	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10501394	1.00[CEU][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231535	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231543	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231545	1.00[CEU][hapmap]
rs11551942	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11551944	0.91[CEU][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11820129	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1186941	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1211688	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12274980	1.00[CEU][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17158453	1.00[CEU][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17656941	1.00[CEU][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1789219	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2509744	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959876	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959880	1.00[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959886	0.92[EUR][1000 genomes]
rs3016865	1.00[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34109368	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35345497	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35754698	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs474548	0.85[MEX][hapmap]
rs476034	1.00[CEU][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs476691	1.00[CEU][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs482915	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs484619	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs491231	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs500726	0.93[EUR][1000 genomes]
rs500991	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs511819	1.00[CEU][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs515645	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs517700	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs518490	1.00[CEU][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs518692	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs521464	1.00[CEU][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs523093	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs523809	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs534505	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs534876	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs539306	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs541809	0.88[EUR][1000 genomes]
rs542998	0.85[MEX][hapmap]
rs550629	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs551466	1.00[CEU][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs557882	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs559405	0.90[EUR][1000 genomes]
rs560938	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs562549	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs566255	0.85[MEX][hapmap]
rs566813	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs567756	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs568769	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs568790	1.00[CEU][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs580695	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs588523	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928162	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928163	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928165	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928166	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928167	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928168	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928195	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928196	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928197	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928202	0.96[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928203	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928204	0.96[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928205	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928206	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928208	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928209	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928211	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928212	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928214	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928234	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928236	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928237	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928238	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928239	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928241	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928243	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928244	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928245	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61928246	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928247	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928248	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61929731	0.81[EUR][1000 genomes]
rs6591821	0.95[EUR][1000 genomes]
rs6591822	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7106670	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7111395	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7117206	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7119961	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7127454	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7128040	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7128970	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7928900	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7931908	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7932117	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7939940	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7943981	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7944003	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7944094	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7949389	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7949447	0.85[EUR][1000 genomes];1.00[ASN][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	nsv1051171	chr11:62987064-63835715	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
2	nsv832183	chr11:63416678-63564565	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv897628	chr11:63456478-63508334	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7945972	SNORD25	cis	parietal	SCAN
rs7945972	RASGRP2	cis	parietal	SCAN
rs7945972	SLC22A9	cis	cerebellum	SCAN
rs7945972	PLA2G16	cis	cerebellum	SCAN
rs7945972	MTA2	cis	cerebellum	SCAN
rs7945972	FLRT1	cis	cerebellum	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:63450800-63517400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr11:63451200-63478000	Weak transcription	HSMM	muscle
3	chr11:63451200-63486400	Weak transcription	Primary T cells from cord blood	blood
4	chr11:63451400-63478000	Weak transcription	HSMMtube	muscle
5	chr11:63452000-63486400	Weak transcription	Fetal Thymus	thymus
6	chr11:63456800-63490000	Weak transcription	Primary B cells from cord blood	blood
7	chr11:63457000-63482600	Weak transcription	HepG2	liver
8	chr11:63459600-63516600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr11:63463200-63482000	Weak transcription	Dnd41	blood
10	chr11:63463200-63516200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr11:63464200-63489600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr11:63466200-63490000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr11:63466800-63486800	Weak transcription	Fetal Muscle Trunk	muscle
14	chr11:63467000-63478000	Weak transcription	Right Atrium	heart
15	chr11:63467200-63481600	Weak transcription	Fetal Muscle Leg	muscle
16	chr11:63467400-63478200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr11:63467400-63481400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr11:63467400-63486600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr11:63467400-63497200	Weak transcription	Stomach Smooth Muscle	stomach
20	chr11:63467600-63477600	Weak transcription	Fetal Intestine Large	intestine
21	chr11:63467600-63478000	Weak transcription	Colon Smooth Muscle	Colon
22	chr11:63467600-63485800	Weak transcription	Hela-S3	cervix
23	chr11:63467600-63486200	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr11:63467600-63486400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr11:63467600-63486400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr11:63467600-63486400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr11:63467600-63488200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr11:63467600-63489200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr11:63467600-63489800	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr11:63467600-63516000	Weak transcription	Thymus	Thymus
31	chr11:63467600-63517600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr11:63467800-63486200	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr11:63467800-63486400	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr11:63468200-63480800	Weak transcription	Fetal Brain Female	brain
35	chr11:63469200-63477600	Weak transcription	Fetal Intestine Small	intestine
36	chr11:63469200-63486400	Weak transcription	Psoas Muscle	Psoas
37	chr11:63469400-63482000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr11:63469400-63497600	Weak transcription	Left Ventricle	heart
39	chr11:63470800-63482000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr11:63472400-63479400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr11:63472400-63484000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr11:63472400-63486000	Weak transcription	GM12878-XiMat	blood
43	chr11:63473000-63477600	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr11:63473000-63478000	Weak transcription	Ovary	ovary
45	chr11:63473000-63484000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr11:63473000-63488800	Weak transcription	Esophagus	oesophagus
47	chr11:63473000-63516000	Weak transcription	Lung	lung
48	chr11:63473000-63518000	Weak transcription	Aorta	Aorta
49	chr11:63473000-63529400	Weak transcription	Right Ventricle	heart
50	chr11:63473200-63487200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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