Variant report

Variant	rs7952455
Chromosome Location	chr11:9979761-9979762
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 100 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs11608212	1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs12098983	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12274440	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17271223	1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs17271623	1.00[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17272133	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17292774	1.00[YRI][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17355751	1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs17356069	1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs17356237	1.00[ASN][1000 genomes]
rs17356369	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17358721	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17358882	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4910071	1.00[ASN][1000 genomes]
rs55811615	1.00[ASN][1000 genomes]
rs56067762	1.00[ASN][1000 genomes]
rs61876910	1.00[ASN][1000 genomes]
rs61876915	1.00[ASN][1000 genomes]
rs61876922	1.00[ASN][1000 genomes]
rs61876923	1.00[ASN][1000 genomes]
rs61876926	1.00[ASN][1000 genomes]
rs61876927	1.00[ASN][1000 genomes]
rs61876942	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61876945	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61876948	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61876949	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61876951	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61876972	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61876973	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61876974	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61876975	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61876976	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61876977	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61876978	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61876980	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61876982	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61876983	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61876984	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61877004	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61877005	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61877038	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61877039	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61877042	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61877044	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61877046	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61877050	1.00[ASN][1000 genomes]
rs61877054	1.00[ASN][1000 genomes]
rs61877264	1.00[ASN][1000 genomes]
rs61878586	1.00[ASN][1000 genomes]
rs61878652	0.80[AMR][1000 genomes]
rs61878654	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61878655	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61878657	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61878658	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61878659	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61880160	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6483792	1.00[ASN][1000 genomes]
rs6483859	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66536570	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66553354	1.00[ASN][1000 genomes]
rs7105355	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7108187	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7109648	0.86[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7110027	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7117364	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7118211	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7118427	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7120043	1.00[ASN][1000 genomes]
rs7120403	0.86[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7122370	1.00[ASN][1000 genomes]
rs7123467	0.80[AMR][1000 genomes]
rs7123546	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7129274	1.00[ASN][1000 genomes]
rs7130478	1.00[ASN][1000 genomes]
rs7131546	1.00[ASN][1000 genomes]
rs72854502	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72855652	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72855680	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72857108	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72858820	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72858863	1.00[ASN][1000 genomes]
rs72858902	1.00[ASN][1000 genomes]
rs7342224	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7928664	1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs7935235	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7935610	1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs7936602	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7938570	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7938773	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7939096	1.00[ASN][1000 genomes]
rs7939269	1.00[ASN][1000 genomes]
rs7942807	1.00[ASN][1000 genomes]
rs7945309	1.00[CEU][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7949110	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7949493	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9666488	0.87[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv896988	chr11:9912052-10012511	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv896989	chr11:9951968-10059623	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	esv1819684	chr11:9973062-10012511	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7952455	ARFIP2	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9943400-9980600	Weak transcription	Primary T cells from cord blood	blood
2	chr11:9950200-9980400	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr11:9952800-9980200	Weak transcription	Aorta	Aorta
4	chr11:9952800-9980400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr11:9952800-9980600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr11:9952800-9980600	Weak transcription	Spleen	Spleen
7	chr11:9952800-9995200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr11:9953000-9980200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr11:9953000-9980200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr11:9953000-9980400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr11:9953000-9980400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr11:9953000-9980400	Weak transcription	Esophagus	oesophagus
13	chr11:9964400-9980200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr11:9964800-9980400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr11:9965200-9981000	Weak transcription	HUVEC	blood vessel
16	chr11:9965400-9980200	Weak transcription	Liver	Liver
17	chr11:9966000-9980200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr11:9966000-9980200	Weak transcription	NHLF	lung
19	chr11:9966200-9980200	Weak transcription	Osteobl	bone
20	chr11:9967600-9980200	Weak transcription	Fetal Intestine Large	intestine
21	chr11:9967600-9980400	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr11:9967800-9980200	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr11:9967800-9980200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr11:9967800-9980200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr11:9967800-9980400	Weak transcription	Primary hematopoietic stem cells	blood
26	chr11:9968000-9980200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr11:9968000-9980400	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr11:9968000-9980400	Weak transcription	Dnd41	blood
29	chr11:9968000-9984000	Weak transcription	Primary B cells from cord blood	blood
30	chr11:9968000-9984200	Weak transcription	Fetal Kidney	kidney
31	chr11:9968200-9980200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr11:9968200-9980200	Weak transcription	Rectal Smooth Muscle	rectum
33	chr11:9968200-9980400	Weak transcription	Brain Angular Gyrus	brain
34	chr11:9968400-9980400	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr11:9968600-9980200	Weak transcription	Fetal Brain Female	brain
36	chr11:9969200-9980400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr11:9969400-9980200	Weak transcription	Ovary	ovary
38	chr11:9969400-9980400	Weak transcription	Brain Substantia Nigra	brain
39	chr11:9970800-9980200	Weak transcription	Right Ventricle	heart
40	chr11:9972400-9980200	Weak transcription	Fetal Intestine Small	intestine
41	chr11:9972400-9980200	Weak transcription	Placenta	Placenta
42	chr11:9972800-9980600	Weak transcription	Gastric	stomach
43	chr11:9973000-9986000	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr11:9973200-9980400	Weak transcription	HepG2	liver
45	chr11:9973800-10010600	Weak transcription	Fetal Brain Male	brain
46	chr11:9974000-9980200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr11:9974000-9980400	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr11:9974000-9980400	Weak transcription	Brain Anterior Caudate	brain
49	chr11:9974200-9980200	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr11:9974200-9980200	Weak transcription	Colon Smooth Muscle	Colon

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