Variant report

Variant	rs3892490
Chromosome Location	chr4:6996129-6996130
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	chr4:6910242..6912678-chr4:6994521..6998393,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000132405	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10012590	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[ASN][1000 genomes]
rs10025310	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs1048009	0.88[LWK][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs10516181	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10937772	0.88[ASN][1000 genomes]
rs10937774	0.90[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.85[AMR][1000 genomes]
rs10937776	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11732898	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11938701	0.86[ASN][1000 genomes]
rs11944897	0.86[ASN][1000 genomes]
rs12502513	1.00[CHB][hapmap]
rs12503027	0.86[ASN][1000 genomes]
rs12510715	1.00[CHD][hapmap]
rs12642852	0.85[EUR][1000 genomes]
rs13107989	0.86[ASN][1000 genomes]
rs13122119	1.00[CHB][hapmap];0.83[CHD][hapmap];0.80[ASN][1000 genomes]
rs13135912	0.88[EUR][1000 genomes]
rs13148395	0.86[ASN][1000 genomes]
rs13149411	0.80[ASN][1000 genomes]
rs2301817	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs2301818	1.00[CHD][hapmap];0.80[ASN][1000 genomes]
rs2301819	1.00[CHD][hapmap];0.80[ASN][1000 genomes]
rs2359194	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3188939	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[ASN][1000 genomes]
rs34219101	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34221933	0.86[ASN][1000 genomes]
rs34335938	0.80[ASN][1000 genomes]
rs34463709	0.80[ASN][1000 genomes]
rs34481892	0.80[ASN][1000 genomes]
rs34959511	0.80[ASN][1000 genomes]
rs35170004	0.80[ASN][1000 genomes]
rs3857171	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3894945	0.86[ASN][1000 genomes]
rs4234791	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs4234793	0.86[ASN][1000 genomes]
rs4296677	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4428285	0.95[CEU][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4458452	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4544710	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs4645214	0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4689059	0.83[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4689060	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4689560	1.00[CHB][hapmap]
rs4689563	0.80[ASN][1000 genomes]
rs4689564	0.80[ASN][1000 genomes]
rs4689565	0.80[ASN][1000 genomes]
rs4689568	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4689573	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4689575	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs4689579	0.80[ASN][1000 genomes]
rs55822670	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62289166	0.86[ASN][1000 genomes]
rs66530709	0.80[ASN][1000 genomes]
rs66640699	0.80[ASN][1000 genomes]
rs66931928	0.80[ASN][1000 genomes]
rs66992702	0.80[ASN][1000 genomes]
rs6811496	0.86[ASN][1000 genomes]
rs6816882	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6818744	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs6831129	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6834102	0.86[ASN][1000 genomes]
rs6840780	0.86[ASN][1000 genomes]
rs6854776	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[ASN][1000 genomes]
rs73202120	0.82[AFR][1000 genomes]
rs7655563	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7655773	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs7658198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7661462	0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7661952	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs7673901	0.86[ASN][1000 genomes]
rs7675524	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7685667	0.86[ASN][1000 genomes]
rs7693321	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8180337	0.83[ASW][hapmap];0.95[CEU][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9291126	0.85[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878530	chr4:6888932-7058473	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv34033	chr4:6973270-7390621	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv2757919	chr4:6988148-7269901	Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	esv2759221	chr4:6988148-7269901	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv428436	chr4:6988148-7269901	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3892490	HMX1	cis	parietal	SCAN
rs3892490	GRPEL1	cis	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:6989800-6998000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr4:6990000-6997400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:6990400-7008800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr4:6991000-7021800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:6991400-7000800	Weak transcription	Colonic Mucosa	Colon
6	chr4:6991600-7000000	Weak transcription	Hela-S3	cervix
7	chr4:6993200-6999000	Strong transcription	Dnd41	blood
8	chr4:6993200-7006800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr4:6993800-6998800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr4:6993800-7008400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr4:6994000-6996600	Weak transcription	Left Ventricle	heart
12	chr4:6994000-6996600	Weak transcription	NHDF-Ad	bronchial
13	chr4:6994000-6998000	Weak transcription	Aorta	Aorta
14	chr4:6994000-6998200	Weak transcription	Ovary	ovary
15	chr4:6994000-7000200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr4:6994000-7005200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr4:6994000-7008600	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr4:6994000-7035600	Strong transcription	Fetal Stomach	stomach
19	chr4:6994000-7043200	Weak transcription	Right Atrium	heart
20	chr4:6994200-6996600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr4:6994200-6996600	Weak transcription	Lung	lung
22	chr4:6994200-6996600	Weak transcription	Right Ventricle	heart
23	chr4:6994200-6996800	Weak transcription	Rectal Smooth Muscle	rectum
24	chr4:6994200-6998400	Weak transcription	Small Intestine	intestine
25	chr4:6994200-7000400	Weak transcription	Fetal Heart	heart
26	chr4:6994200-7000600	Strong transcription	Fetal Muscle Leg	muscle
27	chr4:6994200-7035400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr4:6994400-6996200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
29	chr4:6994400-6996200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr4:6994400-6996400	Weak transcription	Fetal Brain Female	brain
31	chr4:6994400-6996600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr4:6994400-6996600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr4:6994400-6998200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr4:6994400-6999600	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr4:6994400-7000800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr4:6994400-7000800	Weak transcription	Pancreas	Pancrea
37	chr4:6994400-7001000	Strong transcription	Fetal Muscle Trunk	muscle
38	chr4:6994400-7013400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr4:6994600-6996200	Weak transcription	NHLF	lung
40	chr4:6994600-6996600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr4:6994600-6996600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr4:6994600-6998000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr4:6994600-6998000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr4:6994600-6998200	Weak transcription	Gastric	stomach
45	chr4:6994600-6998200	Weak transcription	Spleen	Spleen
46	chr4:6994600-6999600	Strong transcription	Primary T cells from cord blood	blood
47	chr4:6994600-6999600	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr4:6994600-7000200	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr4:6994600-7006800	Strong transcription	Stomach Smooth Muscle	stomach
50	chr4:6994600-7021400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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