Variant report

Variant	rs4678438
Chromosome Location	chr3:136344920-136344921
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:136340612..136342191-chr3:136342513..136345195,2	MCF-7	breast:
2	chr3:136342393..136347212-chr3:136468546..136473681,8	MCF-7	breast:
3	chr3:136343802..136345688-chr3:136349798..136351830,2	MCF-7	breast:
4	chr3:136344242..136347550-chr3:136468840..136471507,4	MCF-7	breast:
5	chr3:136341644..136343243-chr3:136343703..136345406,2	K562	blood:
6	chr3:136344155..136348284-chr3:136354109..136358125,4	MCF-7	breast:
7	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: 78 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1017881	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1070232	0.90[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs10935183	0.87[JPT][hapmap]
rs10935184	1.00[JPT][hapmap]
rs10935186	0.93[JPT][hapmap]
rs11715257	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs11919030	0.93[JPT][hapmap]
rs12492510	0.87[JPT][hapmap]
rs12630999	0.90[CEU][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12635723	1.00[ASW][hapmap];0.90[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13068119	0.80[CEU][hapmap];0.83[MEX][hapmap]
rs13433980	0.81[LWK][hapmap];0.92[YRI][hapmap]
rs1394092	0.87[ASW][hapmap];0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap]
rs1484250	0.92[YRI][hapmap]
rs1681818	0.85[CEU][hapmap];1.00[MEX][hapmap]
rs16843991	0.89[YRI][hapmap]
rs1729951	0.87[JPT][hapmap]
rs2062322	0.93[JPT][hapmap]
rs34553037	0.80[CEU][hapmap];0.89[MEX][hapmap]
rs34602896	0.85[CEU][hapmap];0.94[MEX][hapmap];0.81[EUR][1000 genomes]
rs34967300	0.80[CEU][hapmap];0.83[MEX][hapmap]
rs34992220	0.92[CHD][hapmap]
rs35644083	0.85[YRI][hapmap]
rs3856637	0.87[ASW][hapmap];1.00[CEU][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3932048	0.81[YRI][hapmap]
rs4038578	0.93[JPT][hapmap]
rs4336059	0.89[YRI][hapmap]
rs4408829	0.93[JPT][hapmap]
rs4456810	0.87[ASN][1000 genomes]
rs4521165	1.00[JPT][hapmap]
rs4678433	0.87[ASW][hapmap];0.95[CEU][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap]
rs4678437	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57693506	0.89[ASN][1000 genomes]
rs6439642	0.88[YRI][hapmap]
rs6439649	1.00[JPT][hapmap]
rs6765239	0.89[YRI][hapmap]
rs6771713	0.81[LWK][hapmap];0.92[YRI][hapmap]
rs6782151	0.92[YRI][hapmap]
rs6784582	0.85[EUR][1000 genomes]
rs6791142	0.93[JPT][hapmap]
rs6791611	0.87[JPT][hapmap]
rs6794351	0.95[CEU][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs6799699	0.81[LWK][hapmap];0.92[YRI][hapmap]
rs6800969	0.89[YRI][hapmap]
rs6802702	0.93[JPT][hapmap]
rs6808312	1.00[JPT][hapmap]
rs699165	0.93[ASW][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.89[MEX][hapmap];0.89[YRI][hapmap]
rs711975	0.93[JPT][hapmap]
rs7432375	0.93[JPT][hapmap]
rs7616204	0.93[JPT][hapmap]
rs7618518	1.00[JPT][hapmap]
rs7618871	0.93[JPT][hapmap]
rs7621025	0.89[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap]
rs7623824	0.89[YRI][hapmap]
rs7644346	0.81[LWK][hapmap];0.92[YRI][hapmap]
rs7644471	0.89[YRI][hapmap]
rs833752	0.87[ASW][hapmap];0.90[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap]
rs900048	0.87[ASW][hapmap];0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap]
rs900818	0.93[JPT][hapmap]
rs9289511	0.89[CHB][hapmap]
rs940174	0.93[JPT][hapmap]
rs9812319	0.85[YRI][hapmap]
rs9820485	0.89[CHB][hapmap];0.96[CHD][hapmap]
rs9820513	0.89[YRI][hapmap]
rs9821478	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs9833207	0.89[CHB][hapmap];0.92[CHD][hapmap]
rs9836231	0.93[JPT][hapmap]
rs9839574	0.89[YRI][hapmap]
rs9845762	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9845950	0.81[LWK][hapmap];0.92[YRI][hapmap]
rs9854084	0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs9868120	0.92[YRI][hapmap]
rs9869720	0.89[CHB][hapmap];0.82[CHD][hapmap]
rs9869957	0.88[YRI][hapmap]
rs9883916	0.80[CEU][hapmap];0.83[MEX][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4678438	MSL2	cis	cerebellum	SCAN
rs4678438	PCCB	cis	cerebellum	SCAN
rs4678438	NCK1	cis	parietal	SCAN
rs4678438	PCCB	cis	lymphoblastoid	seeQTL

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

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	chr3:136297200-136345400	Weak transcription	Colon Smooth Muscle	Colon
5	chr3:136297200-136351200	Weak transcription	Pancreas	Pancrea
6	chr3:136298600-136351600	Weak transcription	HSMM	muscle
7	chr3:136300200-136351200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:136308000-136357400	Weak transcription	Lung	lung
9	chr3:136315400-136356400	Weak transcription	Brain Anterior Caudate	brain
10	chr3:136315800-136346800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr3:136315800-136355600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr3:136315800-136361000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr3:136316000-136364400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr3:136320800-136356800	Weak transcription	Ovary	ovary
15	chr3:136322200-136355200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:136323200-136347000	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr3:136323400-136347200	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr3:136323400-136362000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:136323800-136347000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr3:136324200-136346600	Weak transcription	Primary B cells from cord blood	blood
21	chr3:136324200-136363600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr3:136327400-136357400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr3:136327800-136346800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr3:136328000-136350200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr3:136328000-136351200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr3:136328200-136346800	Weak transcription	Fetal Muscle Trunk	muscle
27	chr3:136331800-136349400	Weak transcription	NHDF-Ad	bronchial
28	chr3:136331800-136350000	Weak transcription	NHLF	lung
29	chr3:136335600-136349800	Weak transcription	Osteobl	bone
30	chr3:136335600-136350600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr3:136335600-136357400	Weak transcription	Psoas Muscle	Psoas
32	chr3:136335800-136350200	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr3:136336200-136364800	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr3:136336400-136346600	Weak transcription	Adipose Nuclei	Adipose
35	chr3:136336400-136350200	Weak transcription	Gastric	stomach
36	chr3:136336400-136351400	Weak transcription	Right Ventricle	heart
37	chr3:136336600-136346400	Weak transcription	Fetal Thymus	thymus
38	chr3:136338400-136349800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:136338600-136345800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr3:136338800-136346800	Weak transcription	Fetal Muscle Leg	muscle
41	chr3:136338800-136346800	Weak transcription	Thymus	Thymus
42	chr3:136338800-136355600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr3:136339000-136350200	Weak transcription	Fetal Stomach	stomach
44	chr3:136339600-136346800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr3:136339600-136346800	Weak transcription	Primary B cells from peripheral blood	blood
46	chr3:136340400-136346400	Weak transcription	Primary T cells from cord blood	blood
47	chr3:136340800-136349200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:136341200-136346400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr3:136341200-136350000	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr3:136341800-136345400	Weak transcription	Dnd41	blood

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