Variant report

Variant	rs696517
Chromosome Location	chr3:136067655-136067656
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:136062780..136064469-chr3:136066543..136068055,2	K562	blood:
2	chr3:135913544..135916307-chr3:136066201..136068318,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174579	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1145101	1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1145106	0.92[LWK][hapmap];1.00[MEX][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes]
rs1154988	0.88[CEU][hapmap]
rs11715257	0.88[MEX][hapmap]
rs1279425	0.84[CEU][hapmap]
rs1279840	0.84[CEU][hapmap];0.94[MEX][hapmap]
rs13068119	0.89[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap]
rs1394092	0.94[MEX][hapmap]
rs1711171	0.84[CEU][hapmap]
rs17252498	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs28478252	0.81[AFR][1000 genomes]
rs33999043	0.82[EUR][1000 genomes]
rs34154714	1.00[ASN][1000 genomes]
rs34498968	1.00[JPT][hapmap]
rs35087366	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs3755636	0.88[CEU][hapmap]
rs3821445	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs4678428	0.84[CEU][hapmap]
rs4678433	0.94[MEX][hapmap]
rs483465	0.84[ASW][hapmap];0.84[CEU][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes]
rs489398	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs503973	1.00[JPT][hapmap];0.90[AMR][1000 genomes]
rs548288	0.84[CEU][hapmap];0.94[MEX][hapmap]
rs571513	0.84[ASW][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap]
rs576771	0.84[CEU][hapmap];1.00[MEX][hapmap]
rs606725	0.84[CEU][hapmap]
rs610860	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61789601	0.85[EUR][1000 genomes]
rs645040	0.88[CEU][hapmap];0.83[MEX][hapmap]
rs667920	1.00[MEX][hapmap];0.81[YRI][hapmap]
rs684773	0.88[CEU][hapmap];0.88[MEX][hapmap]
rs687339	0.88[CEU][hapmap];0.88[MEX][hapmap]
rs695983	0.94[MEX][hapmap];0.81[YRI][hapmap]
rs696516	0.94[MEX][hapmap]
rs698270	0.84[ASW][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap]
rs699165	0.83[MEX][hapmap]
rs71336055	0.87[ASN][1000 genomes]
rs8045	0.89[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs833752	0.88[MEX][hapmap]
rs866782	0.92[EUR][1000 genomes]
rs900048	0.94[MEX][hapmap]
rs9867368	0.81[AMR][1000 genomes]
rs9883916	0.89[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap]

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	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv948461	chr3:135969755-136349636	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv877519	chr3:136035737-136279390	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv877520	chr3:136056861-136310985	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs696517	MSL2	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136039000-136072400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:136042400-136078800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr3:136042600-136072600	Strong transcription	Dnd41	blood
4	chr3:136043400-136098600	Weak transcription	Fetal Brain Male	brain
5	chr3:136043600-136082000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr3:136043800-136070400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:136045600-136079200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr3:136047600-136098000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr3:136047800-136068200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr3:136047800-136074800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr3:136051000-136069800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr3:136051600-136069200	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr3:136051600-136070800	Strong transcription	Fetal Muscle Trunk	muscle
14	chr3:136052200-136069200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr3:136052800-136070800	Strong transcription	Primary B cells from peripheral blood	blood
16	chr3:136053000-136072400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr3:136053800-136069000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr3:136054200-136085400	Weak transcription	Brain Hippocampus Middle	brain
19	chr3:136054600-136074200	Weak transcription	Brain Angular Gyrus	brain
20	chr3:136054600-136172000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr3:136054800-136076600	Weak transcription	Brain Substantia Nigra	brain
22	chr3:136055400-136069000	Weak transcription	Aorta	Aorta
23	chr3:136055600-136073400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr3:136055600-136100800	Weak transcription	Spleen	Spleen
25	chr3:136057800-136069800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr3:136059000-136072000	Weak transcription	GM12878-XiMat	blood
27	chr3:136059200-136069200	Weak transcription	Psoas Muscle	Psoas
28	chr3:136059600-136070400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:136059600-136079000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr3:136060400-136069200	Weak transcription	Right Ventricle	heart
31	chr3:136061800-136074200	Weak transcription	Brain Germinal Matrix	brain
32	chr3:136063200-136071000	Weak transcription	Fetal Brain Female	brain
33	chr3:136063200-136072200	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr3:136063400-136067800	Weak transcription	HSMM	muscle
35	chr3:136063400-136068600	Weak transcription	NHEK	skin
36	chr3:136063400-136068800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr3:136063400-136069000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr3:136063400-136069000	Weak transcription	Colon Smooth Muscle	Colon
39	chr3:136063400-136069000	Weak transcription	Fetal Heart	heart
40	chr3:136063400-136069000	Weak transcription	Rectal Smooth Muscle	rectum
41	chr3:136063400-136069000	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr3:136063400-136069000	Weak transcription	Thymus	Thymus
43	chr3:136063400-136069200	Weak transcription	Esophagus	oesophagus
44	chr3:136063400-136069200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr3:136063400-136069200	Weak transcription	Stomach Smooth Muscle	stomach
46	chr3:136063400-136071800	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr3:136063400-136072200	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr3:136063400-136072200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr3:136063400-136073800	Weak transcription	Primary hematopoietic stem cells	blood
50	chr3:136063400-136139000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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