Variant report

Variant	rs6034464
Chromosome Location	chr20:16359567-16359568
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:16358739..16360816-chr20:16361269..16364675,3	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs12624939	1.00[JPT][hapmap]
rs1884598	1.00[ASW][hapmap];0.96[CEU][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1884604	0.83[CHD][hapmap]
rs1884606	0.83[CHD][hapmap]
rs2144883	0.83[CHD][hapmap]
rs2144885	0.89[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2144886	0.89[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2144887	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2144888	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2144889	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2144890	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2144891	0.89[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2180442	1.00[JPT][hapmap]
rs2180443	0.89[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2208056	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2328020	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2876428	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs4814477	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4814478	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4814482	0.81[CEU][hapmap];0.82[GIH][hapmap];0.91[MKK][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs6034466	0.89[ASW][hapmap];0.81[CEU][hapmap];0.82[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6043882	0.83[CHD][hapmap]
rs6043911	0.89[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6043913	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6075051	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6080243	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6080244	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6105582	1.00[JPT][hapmap]
rs6105603	1.00[JPT][hapmap]
rs6111075	0.89[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6111076	0.86[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6135738	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6135739	0.89[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7268027	1.00[JPT][hapmap]
rs7271622	1.00[JPT][hapmap]
rs7272048	1.00[JPT][hapmap]
rs8117949	1.00[JPT][hapmap]
rs8122535	1.00[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833931	chr20:16308276-16460596	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6034464	SPTLC3	cis	cerebellum	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:16315400-16364400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr20:16316000-16384400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr20:16318800-16368200	Weak transcription	Primary B cells from cord blood	blood
4	chr20:16334000-16377400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr20:16341200-16371600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr20:16342600-16377400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr20:16343600-16366800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr20:16343600-16384600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr20:16344400-16380200	Weak transcription	HSMMtube	muscle
10	chr20:16344800-16360800	Strong transcription	Rectal Mucosa Donor 31	rectum
11	chr20:16344800-16371400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr20:16344800-16377400	Weak transcription	Brain Angular Gyrus	brain
13	chr20:16345000-16391200	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr20:16345400-16377400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr20:16345400-16391000	Weak transcription	Brain Germinal Matrix	brain
16	chr20:16346400-16363200	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr20:16346600-16362400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr20:16346600-16393600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr20:16346800-16359600	Weak transcription	Placenta	Placenta
20	chr20:16347200-16368200	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr20:16347400-16360000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr20:16347600-16392000	Weak transcription	Fetal Kidney	kidney
23	chr20:16348400-16383600	Weak transcription	Small Intestine	intestine
24	chr20:16348800-16361800	Weak transcription	Thymus	Thymus
25	chr20:16349000-16371800	Weak transcription	Stomach Mucosa	stomach
26	chr20:16349200-16365000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr20:16349200-16380000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr20:16349400-16364200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr20:16349600-16372200	Weak transcription	Colonic Mucosa	Colon
30	chr20:16349600-16376400	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr20:16349800-16362800	Weak transcription	Osteobl	bone
32	chr20:16349800-16381600	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr20:16350000-16360200	Weak transcription	Primary B cells from peripheral blood	blood
34	chr20:16350000-16361800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr20:16350000-16363000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr20:16350000-16366200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr20:16350000-16384000	Weak transcription	HepG2	liver
38	chr20:16350000-16384200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr20:16350200-16368200	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr20:16350600-16362200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr20:16350600-16375000	Weak transcription	Colon Smooth Muscle	Colon
42	chr20:16350800-16360000	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr20:16350800-16384200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr20:16352000-16360800	Strong transcription	Stomach Smooth Muscle	stomach
45	chr20:16352000-16361000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr20:16352200-16361800	Strong transcription	Duodenum Mucosa	Duodenum
47	chr20:16352600-16361400	Strong transcription	Primary T cells from cord blood	blood
48	chr20:16353000-16384200	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr20:16353800-16361600	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr20:16354200-16361200	Strong transcription	Duodenum Smooth Muscle	Duodenum

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