Variant report

Variant	rs34602896
Chromosome Location	chr3:136346385-136346386
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:136342393..136347212-chr3:136468546..136473681,8	MCF-7	breast:
2	chr3:136344242..136347550-chr3:136468840..136471507,4	MCF-7	breast:
3	chr3:136344155..136348284-chr3:136354109..136358125,4	MCF-7	breast:
4	chr3:136344347..136346500-chr3:136421190..136423734,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000118007	Chromatin interaction
ENSG00000261758	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11715257	0.88[MEX][hapmap]
rs12630999	0.88[MEX][hapmap]
rs13063893	1.00[ASN][1000 genomes]
rs13068119	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.86[YRI][hapmap]
rs13069695	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs13072691	1.00[CHD][hapmap]
rs1394092	0.83[MEX][hapmap]
rs1681818	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap]
rs34498968	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs34553037	0.87[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34967300	0.87[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap]
rs3856637	0.85[CEU][hapmap];0.94[MEX][hapmap]
rs4678433	0.83[MEX][hapmap]
rs4678437	0.85[CEU][hapmap];0.89[MEX][hapmap]
rs4678438	0.85[CEU][hapmap];0.94[MEX][hapmap];0.81[EUR][1000 genomes]
rs6794351	0.88[MEX][hapmap]
rs699165	0.83[MEX][hapmap]
rs7621025	0.83[MEX][hapmap]
rs833752	0.88[MEX][hapmap]
rs900048	0.83[MEX][hapmap]
rs9845762	0.85[CEU][hapmap];0.94[MEX][hapmap]
rs9861150	0.93[YRI][hapmap]
rs9883916	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.93[YRI][hapmap]

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	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
2	nsv460861	chr3:136222954-136425600	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv591851	chr3:136222954-136425600	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs34602896	MSL2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136248200-136349200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr3:136268200-136351200	Weak transcription	Esophagus	oesophagus
3	chr3:136290000-136351600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:136297200-136351200	Weak transcription	Pancreas	Pancrea
5	chr3:136298600-136351600	Weak transcription	HSMM	muscle
6	chr3:136300200-136351200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:136308000-136357400	Weak transcription	Lung	lung
8	chr3:136315400-136356400	Weak transcription	Brain Anterior Caudate	brain
9	chr3:136315800-136346800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr3:136315800-136355600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr3:136315800-136361000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr3:136316000-136364400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr3:136320800-136356800	Weak transcription	Ovary	ovary
14	chr3:136322200-136355200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:136323200-136347000	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr3:136323400-136347200	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr3:136323400-136362000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:136323800-136347000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr3:136324200-136346600	Weak transcription	Primary B cells from cord blood	blood
20	chr3:136324200-136363600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr3:136327400-136357400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr3:136327800-136346800	Weak transcription	Primary hematopoietic stem cells	blood
23	chr3:136328000-136350200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr3:136328000-136351200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr3:136328200-136346800	Weak transcription	Fetal Muscle Trunk	muscle
26	chr3:136331800-136349400	Weak transcription	NHDF-Ad	bronchial
27	chr3:136331800-136350000	Weak transcription	NHLF	lung
28	chr3:136335600-136349800	Weak transcription	Osteobl	bone
29	chr3:136335600-136350600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr3:136335600-136357400	Weak transcription	Psoas Muscle	Psoas
31	chr3:136335800-136350200	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr3:136336200-136364800	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr3:136336400-136346600	Weak transcription	Adipose Nuclei	Adipose
34	chr3:136336400-136350200	Weak transcription	Gastric	stomach
35	chr3:136336400-136351400	Weak transcription	Right Ventricle	heart
36	chr3:136336600-136346400	Weak transcription	Fetal Thymus	thymus
37	chr3:136338400-136349800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:136338800-136346800	Weak transcription	Fetal Muscle Leg	muscle
39	chr3:136338800-136346800	Weak transcription	Thymus	Thymus
40	chr3:136338800-136355600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr3:136339000-136350200	Weak transcription	Fetal Stomach	stomach
42	chr3:136339600-136346800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr3:136339600-136346800	Weak transcription	Primary B cells from peripheral blood	blood
44	chr3:136340400-136346400	Weak transcription	Primary T cells from cord blood	blood
45	chr3:136340800-136349200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr3:136341200-136346400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:136341200-136350000	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr3:136342200-136355600	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr3:136342400-136346600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:136342600-136346600	Weak transcription	Primary T helper cells fromperipheralblood	blood

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