Variant report

Variant	rs6550373
Chromosome Location	chr3:20195962-20195963
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:20195318..20197314-chr3:20202622..20204510,2	MCF-7	breast:
2	chr3:20191414..20193219-chr3:20194880..20197331,2	K562	blood:
3	chr3:20177373..20179838-chr3:20195136..20197383,2	K562	blood:
4	chr3:20193485..20196421-chr3:20205590..20208525,2	K562	blood:

Variant related genes	Relation type
ENSG00000266745	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1052930	0.85[CHD][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap];0.88[ASN][1000 genomes]
rs1828080	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1848322	0.88[ASN][1000 genomes]
rs1848323	0.88[ASN][1000 genomes]
rs1868	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1995722	0.85[CHD][hapmap];0.88[ASN][1000 genomes]
rs2140085	0.84[AMR][1000 genomes]
rs2661378	1.00[CHD][hapmap];0.89[MEX][hapmap];0.87[AMR][1000 genomes]
rs2686313	1.00[CHD][hapmap]
rs2686314	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs2686316	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2686317	1.00[CHD][hapmap];0.89[MEX][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3852067	0.85[CHD][hapmap];0.88[ASN][1000 genomes]
rs4364184	0.88[ASN][1000 genomes]
rs4435663	1.00[ASW][hapmap];1.00[CHD][hapmap];0.83[MEX][hapmap];0.81[AFR][1000 genomes]
rs4491921	0.88[ASN][1000 genomes]
rs4858158	0.88[ASN][1000 genomes]
rs4858778	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs57625405	0.88[ASN][1000 genomes]
rs6419828	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6550374	0.88[ASN][1000 genomes]
rs6550402	0.88[ASN][1000 genomes]
rs6550403	0.88[ASN][1000 genomes]
rs6550410	0.88[ASN][1000 genomes]
rs6550412	0.88[ASN][1000 genomes]
rs6550423	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6767049	0.88[ASN][1000 genomes]
rs6773807	0.88[ASN][1000 genomes]
rs6777450	0.88[ASN][1000 genomes]
rs6793304	0.85[CHD][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap];0.88[ASN][1000 genomes]
rs6796884	0.88[ASN][1000 genomes]
rs6809221	0.83[ASN][1000 genomes]
rs7619317	0.85[CHD][hapmap];0.88[ASN][1000 genomes]
rs7624514	1.00[CHD][hapmap]
rs7628915	0.85[CHD][hapmap];0.82[GIH][hapmap];0.88[MKK][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7635559	0.88[ASN][1000 genomes]
rs9310613	0.85[CHD][hapmap];0.88[ASN][1000 genomes]
rs9310615	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs951455	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs955011	0.88[ASN][1000 genomes]
rs970589	0.88[ASN][1000 genomes]
rs978928	0.88[ASN][1000 genomes]
rs9810567	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9849205	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv1826830	chr3:19982972-20632072	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	esv1829542	chr3:20009231-20384627	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv834627	chr3:20068115-20227975	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv433359	chr3:20090908-20587572	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv470450	chr3:20096735-20389045	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv1001006	chr3:20110743-20752628	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv536512	chr3:20110743-20752628	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	esv1829018	chr3:20116077-20596244	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
11	esv1827700	chr3:20119716-20489086	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
12	esv1830036	chr3:20121828-20278275	Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
13	esv1830599	chr3:20121828-20375643	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
14	esv1828816	chr3:20136508-20389045	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
15	esv3394910	chr3:20150394-20203576	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
16	esv3334928	chr3:20150414-20203546	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
17	esv1832674	chr3:20152772-20605302	Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
18	esv1831853	chr3:20157077-20615273	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
19	esv1833208	chr3:20157077-20638228	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
20	esv2422249	chr3:20163608-20626956	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
21	esv1826144	chr3:20164282-20638228	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
22	nsv1013532	chr3:20172889-20305612	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
23	nsv536513	chr3:20172889-20305612	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
24	nsv237514	chr3:20191013-20198743	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS	Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
25	esv1831289	chr3:20191506-20617984	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
26	esv1829973	chr3:20192578-20375260	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6550373	SGOL1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:20141200-20222400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:20151000-20196800	Weak transcription	Stomach Mucosa	stomach
3	chr3:20159200-20201400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:20162800-20198200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:20164400-20204400	Weak transcription	Small Intestine	intestine
6	chr3:20164800-20211400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:20167800-20196600	Weak transcription	K562	blood
8	chr3:20167800-20226000	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr3:20168800-20200800	Weak transcription	GM12878-XiMat	blood
10	chr3:20169600-20198400	Weak transcription	Aorta	Aorta
11	chr3:20169600-20198400	Weak transcription	Pancreas	Pancrea
12	chr3:20169800-20201600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr3:20169800-20202000	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr3:20175800-20196800	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr3:20179000-20196400	Weak transcription	HUVEC	blood vessel
16	chr3:20179400-20197600	Weak transcription	Right Atrium	heart
17	chr3:20181800-20200200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:20182400-20196400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr3:20182600-20201400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr3:20182800-20198000	Weak transcription	Ovary	ovary
21	chr3:20183600-20201000	Weak transcription	Fetal Muscle Trunk	muscle
22	chr3:20183800-20196000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:20183800-20196000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr3:20183800-20196400	Weak transcription	Fetal Intestine Small	intestine
25	chr3:20183800-20196800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:20183800-20198000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr3:20183800-20198400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr3:20183800-20199600	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr3:20183800-20199600	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr3:20184000-20196400	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr3:20184000-20198000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr3:20184200-20196400	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr3:20184400-20196000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr3:20184400-20197800	Weak transcription	Lung	lung
35	chr3:20184400-20198000	Weak transcription	Right Ventricle	heart
36	chr3:20184400-20198400	Weak transcription	Spleen	Spleen
37	chr3:20184400-20198600	Weak transcription	Brain Hippocampus Middle	brain
38	chr3:20184400-20199000	Weak transcription	Esophagus	oesophagus
39	chr3:20184600-20220200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:20184800-20196400	Weak transcription	Gastric	stomach
41	chr3:20187400-20197600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr3:20187400-20197600	Strong transcription	Liver	Liver
43	chr3:20187400-20201000	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr3:20187600-20201200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr3:20188000-20198600	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr3:20188200-20196400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr3:20188400-20204800	Weak transcription	Fetal Brain Female	brain
48	chr3:20188400-20212400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr3:20189000-20196600	Weak transcription	Rectal Smooth Muscle	rectum
50	chr3:20189000-20196800	Strong transcription	Primary hematopoietic stem cells	blood

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