Variant report

Variant	rs3929738
Chromosome Location	chr1:67397865-67397866
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	chr1:67389047..67393171-chr1:67393255..67399137,11	MCF-7	breast:
2	chr1:67385997..67392679-chr1:67394416..67400305,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152763	Chromatin interaction
ENSG00000198160	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10749766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10789219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10889651	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1118392	0.92[CEU][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes]
rs11208971	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11208973	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11208974	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11208979	0.90[JPT][hapmap]
rs1121824	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12041926	0.90[JPT][hapmap]
rs12044278	0.92[JPT][hapmap]
rs12131222	0.92[JPT][hapmap]
rs12137403	0.90[JPT][hapmap]
rs12562761	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12742428	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1535365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs1570838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17497828	0.90[JPT][hapmap]
rs1925408	0.90[JPT][hapmap]
rs1925409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1925410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1925411	0.92[JPT][hapmap]
rs1925413	0.92[JPT][hapmap]
rs2025608	0.92[JPT][hapmap]
rs2065000	0.92[JPT][hapmap]
rs2065001	0.90[JPT][hapmap]
rs2065002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2182143	0.90[JPT][hapmap]
rs2755241	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2755242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2755243	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2755244	0.90[JPT][hapmap]
rs2755245	0.90[JPT][hapmap]
rs2755246	0.90[JPT][hapmap]
rs2755250	0.92[JPT][hapmap]
rs2755251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs2755253	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2755254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2755256	0.82[JPT][hapmap]
rs2755266	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2755270	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2755271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2815349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2815351	0.90[JPT][hapmap]
rs2815355	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2815359	0.90[JPT][hapmap]
rs2815360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2815361	0.90[JPT][hapmap]
rs2815362	0.85[EUR][1000 genomes]
rs2815363	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs2815364	0.85[EUR][1000 genomes]
rs2815365	0.85[EUR][1000 genomes]
rs2815366	0.85[EUR][1000 genomes]
rs2815367	0.85[EUR][1000 genomes]
rs2815368	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs2815370	0.90[JPT][hapmap]
rs2815371	0.90[JPT][hapmap]
rs2815374	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2985795	0.92[JPT][hapmap]
rs2985797	0.90[JPT][hapmap]
rs2985818	0.90[JPT][hapmap]
rs2985821	0.92[JPT][hapmap]
rs2985822	0.90[JPT][hapmap]
rs2985824	0.90[JPT][hapmap]
rs2985825	0.90[JPT][hapmap]
rs2985826	0.92[JPT][hapmap]
rs3008848	0.90[JPT][hapmap]
rs3008853	0.92[JPT][hapmap]
rs3008854	0.92[JPT][hapmap]
rs3008855	0.90[JPT][hapmap]
rs3008858	0.92[JPT][hapmap]
rs3008871	0.81[JPT][hapmap]
rs3008892	0.90[JPT][hapmap]
rs3736905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4486425	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4570393	0.85[EUR][1000 genomes]
rs4581250	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4582760	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4620509	0.92[JPT][hapmap]
rs4655658	0.92[JPT][hapmap]
rs4655660	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4655661	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4655662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4655663	0.90[JPT][hapmap]
rs6657065	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6673462	0.92[JPT][hapmap]
rs912797	0.90[JPT][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	nsv869413	chr1:67082512-67414286	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv871720	chr1:67357596-67435161	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv947266	chr1:67358868-67399427	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3929738	SLC35D1	Cis_1M	lymphoblastoid	RTeQTL
rs3929738	MIER1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67395000-67398800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:67395000-67401400	Active TSS	K562	blood
3	chr1:67395200-67398000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:67395200-67398000	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr1:67395200-67398200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:67395200-67398400	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr1:67395200-67398600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:67395200-67398600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:67395400-67398000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:67395400-67398000	Active TSS	Primary T killer memory cells from peripheral blood	blood
11	chr1:67395400-67398000	Active TSS	Stomach Mucosa	stomach
12	chr1:67395400-67398200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:67395400-67398200	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr1:67395400-67399000	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr1:67395400-67400200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:67395400-67401000	Active TSS	A549	lung
17	chr1:67395600-67398000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:67395600-67398000	Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr1:67395600-67398000	Active TSS	NHEK	skin
20	chr1:67395600-67398200	Active TSS	Liver	Liver
21	chr1:67395600-67399200	Active TSS	GM12878-XiMat	blood
22	chr1:67395600-67400000	Active TSS	Primary T cells fromperipheralblood	blood
23	chr1:67395600-67400000	Active TSS	HMEC	breast
24	chr1:67395600-67400400	Active TSS	NHLF	lung
25	chr1:67395600-67400600	Active TSS	Hela-S3	cervix
26	chr1:67395800-67398000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:67396400-67398200	Flanking Active TSS	Primary B cells from cord blood	blood
28	chr1:67396600-67398000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
29	chr1:67396600-67398800	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
30	chr1:67396600-67416600	Weak transcription	Spleen	Spleen
31	chr1:67396800-67398200	Active TSS	HepG2	liver
32	chr1:67396800-67398400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
33	chr1:67396800-67400000	Weak transcription	Left Ventricle	heart
34	chr1:67396800-67403000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr1:67396800-67403000	Weak transcription	Gastric	stomach
36	chr1:67396800-67411200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr1:67396800-67414400	Weak transcription	Lung	lung
38	chr1:67396800-67429800	Weak transcription	Pancreas	Pancrea
39	chr1:67396800-67458200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:67396800-67459000	Weak transcription	Esophagus	oesophagus
41	chr1:67397000-67398200	Flanking Active TSS	Fetal Lung	lung
42	chr1:67397000-67398400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr1:67397000-67399000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
44	chr1:67397000-67400400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:67397000-67400600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr1:67397000-67408000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr1:67397000-67409200	Weak transcription	Fetal Muscle Trunk	muscle
48	chr1:67397200-67398400	Flanking Active TSS	NH-A	brain
49	chr1:67397200-67398800	Flanking Active TSS	HUVEC	blood vessel
50	chr1:67397200-67400200	Flanking Active TSS	Osteobl	bone

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