Variant report

Variant	rs3756443
Chromosome Location	chr5:73987546-73987547
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:73987539-73987876	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:73986659..73988888-chr5:73994649..73997081,2	MCF-7	breast:
2	chr5:73979909..73982593-chr5:73987219..73990536,5	MCF-7	breast:
3	chr5:73979598..73982392-chr5:73983812..73990818,9	MCF-7	breast:
4	chr5:73979743..73983565-chr5:73984545..73990071,12	K562	blood:

Variant related genes	Relation type
HEXB	TF binding region
ENSG00000049860	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10942718	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11556045	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12517888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12518926	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12519436	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12521189	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13154639	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13178702	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13188271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1566431	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872206	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35711978	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733791	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3776484	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56320720	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62368221	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6453073	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7710892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs820875	0.84[AFR][1000 genomes]
rs820880	0.85[MKK][hapmap]
rs820883	0.85[MKK][hapmap]
rs820885	0.85[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv13844	chr5:73979961-73993853	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
2	nsv598652	chr5:73980182-73992881	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
3	nsv934214	chr5:73981349-73993050	Active TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
4	nsv933165	chr5:73981599-73993050	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3756443	HEXB	cis	parietal	SCAN
rs3756443	HEXB	cis	cerebellum	SCAN
rs3756443	HEXB	cis	lymphoblastoid	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:73982000-73988800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr5:73982000-73989000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr5:73982000-73994400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:73982000-74002200	Weak transcription	Fetal Brain Female	brain
5	chr5:73982000-74017400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr5:73982000-74061800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:73982200-74020600	Weak transcription	Fetal Brain Male	brain
8	chr5:73982400-73988000	Weak transcription	Fetal Stomach	stomach
9	chr5:73982400-73988400	Weak transcription	Fetal Muscle Leg	muscle
10	chr5:73982400-73989000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr5:73982400-73989200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr5:73982400-73989200	Weak transcription	HSMMtube	muscle
13	chr5:73982400-73989600	Weak transcription	Fetal Thymus	thymus
14	chr5:73982400-73989800	Weak transcription	Thymus	Thymus
15	chr5:73982400-73993000	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr5:73982400-73994600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr5:73982400-73998200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr5:73982400-73999400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr5:73982400-74002200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr5:73982600-73988200	Weak transcription	Ovary	ovary
21	chr5:73982600-73999400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr5:73983000-73988200	Weak transcription	Brain Substantia Nigra	brain
23	chr5:73983000-73988400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr5:73983000-73991800	Weak transcription	Colon Smooth Muscle	Colon
25	chr5:73983000-74001000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr5:73983000-74001600	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr5:73983000-74017400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr5:73983000-74027000	Weak transcription	Fetal Heart	heart
29	chr5:73983200-73988200	Weak transcription	Rectal Smooth Muscle	rectum
30	chr5:73983200-73988400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr5:73983200-73988400	Weak transcription	Spleen	Spleen
32	chr5:73983200-73989000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr5:73983200-73989000	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr5:73983200-73989200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr5:73983200-73989200	Weak transcription	Aorta	Aorta
36	chr5:73983200-73992800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr5:73983200-73992800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr5:73983200-73993000	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr5:73983200-73993000	Weak transcription	GM12878-XiMat	blood
40	chr5:73983200-73994800	Weak transcription	Gastric	stomach
41	chr5:73983200-74002200	Weak transcription	Esophagus	oesophagus
42	chr5:73983200-74030200	Weak transcription	Small Intestine	intestine
43	chr5:73983400-73987800	Weak transcription	Right Ventricle	heart
44	chr5:73983400-73988000	Weak transcription	Left Ventricle	heart
45	chr5:73983400-73988200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr5:73983400-73988600	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr5:73983400-73988600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr5:73983400-73988800	Weak transcription	Pancreas	Pancrea
49	chr5:73983400-73988800	Weak transcription	NH-A	brain
50	chr5:73983400-73989000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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