Variant report

Variant	rs820876
Chromosome Location	chr5:73987048-73987049
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

Variant related genes	Relation type
ENSG00000049860	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs2936918	0.96[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes]
rs3104693	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6896615	0.87[EUR][1000 genomes]
rs820841	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs820862	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs820863	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs820866	0.96[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.87[EUR][1000 genomes]
rs820868	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs820869	0.96[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs820870	0.96[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs820872	0.96[CEU][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs820874	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs820876	HEXB	cis	parietal	SCAN
rs820876	TMEM174	cis	parietal	SCAN
rs820876	MAP1B	cis	parietal	SCAN
rs820876	HEXB	cis	cerebellum	SCAN

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	chr5:73982200-73987200	Weak transcription	Fetal Lung	lung
8	chr5:73982200-74020600	Weak transcription	Fetal Brain Male	brain
9	chr5:73982400-73988000	Weak transcription	Fetal Stomach	stomach
10	chr5:73982400-73988400	Weak transcription	Fetal Muscle Leg	muscle
11	chr5:73982400-73989000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr5:73982400-73989200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr5:73982400-73989200	Weak transcription	HSMMtube	muscle
14	chr5:73982400-73989600	Weak transcription	Fetal Thymus	thymus
15	chr5:73982400-73989800	Weak transcription	Thymus	Thymus
16	chr5:73982400-73993000	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr5:73982400-73994600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr5:73982400-73998200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr5:73982400-73999400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr5:73982400-74002200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr5:73982600-73988200	Weak transcription	Ovary	ovary
22	chr5:73982600-73999400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr5:73983000-73988200	Weak transcription	Brain Substantia Nigra	brain
24	chr5:73983000-73988400	Weak transcription	Brain Cingulate Gyrus	brain
25	chr5:73983000-73991800	Weak transcription	Colon Smooth Muscle	Colon
26	chr5:73983000-74001000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr5:73983000-74001600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr5:73983000-74017400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr5:73983000-74027000	Weak transcription	Fetal Heart	heart
30	chr5:73983200-73988200	Weak transcription	Rectal Smooth Muscle	rectum
31	chr5:73983200-73988400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr5:73983200-73988400	Weak transcription	Spleen	Spleen
33	chr5:73983200-73989000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr5:73983200-73989000	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr5:73983200-73989200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr5:73983200-73989200	Weak transcription	Aorta	Aorta
37	chr5:73983200-73992800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr5:73983200-73992800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr5:73983200-73993000	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr5:73983200-73993000	Weak transcription	GM12878-XiMat	blood
41	chr5:73983200-73994800	Weak transcription	Gastric	stomach
42	chr5:73983200-74002200	Weak transcription	Esophagus	oesophagus
43	chr5:73983200-74030200	Weak transcription	Small Intestine	intestine
44	chr5:73983400-73987200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr5:73983400-73987800	Weak transcription	Right Ventricle	heart
46	chr5:73983400-73988000	Weak transcription	Left Ventricle	heart
47	chr5:73983400-73988200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr5:73983400-73988600	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr5:73983400-73988600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr5:73983400-73988800	Weak transcription	Pancreas	Pancrea

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