Variant report

Variant	rs28943586
Chromosome Location	chr5:118787669-118787670
allele	A/C
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	CTCF	chr5:118787580-118787730	K562	blood:	n/a	n/a
2	TBP	chr5:118787563-118789017	K562	blood:	n/a	n/a
3	KAP1	chr5:118787129-118789033	HEK293	kidney:	n/a	n/a
4	NR2F2	chr5:118787530-118789239	K562	blood:	n/a	n/a
5	CTCF	chr5:118787560-118787710	GM12873	blood:	n/a	n/a
6	CBX3	chr5:118787133-118788713	K562	blood:	n/a	n/a
7	POLR2A	chr5:118787604-118790194	HepG2	liver:	n/a	n/a
8	HCFC1	chr5:118787556-118789172	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:118323861..118326778-chr5:118787539..118789741,2	MCF-7	breast:
2	chr5:118787302..118789344-chr5:118814419..118817189,2	K562	blood:

Variant related genes	Relation type
HSD17B4	TF binding region
ENSG00000169570	Chromatin interaction
ENSG00000133835	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10059654	0.94[EUR][1000 genomes]
rs10463469	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10463711	0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11744058	0.82[ASN][1000 genomes]
rs11749784	0.87[ASN][1000 genomes]
rs17453681	0.85[EUR][1000 genomes]
rs28943585	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28943593	1.00[AFR][1000 genomes]
rs3756513	0.80[ASN][1000 genomes]
rs55700001	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55901673	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56349852	0.84[EUR][1000 genomes]
rs6898518	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72788170	0.82[ASN][1000 genomes]
rs73249978	0.85[EUR][1000 genomes]
rs73249999	0.85[EUR][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	nsv1030717	chr5:118709310-118836951	Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv427732	chr5:118730999-119034741	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv4974	chr5:118750259-118795376	Genic enhancers Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv1024455	chr5:118770429-119487982	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118781600-118788000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:118785400-118787800	Enhancers	Primary B cells from peripheral blood	blood
3	chr5:118785600-118788000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr5:118786000-118788200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr5:118787200-118788200	Flanking Active TSS	Dnd41	blood
6	chr5:118787200-118789000	Active TSS	Brain Anterior Caudate	brain
7	chr5:118787400-118787800	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr5:118787400-118787800	Enhancers	Primary B cells from cord blood	blood
9	chr5:118787400-118787800	Enhancers	Rectal Mucosa Donor 29	rectum
10	chr5:118787400-118788000	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr5:118787400-118789200	Active TSS	Brain Hippocampus Middle	brain
12	chr5:118787400-118789400	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr5:118787600-118787800	Enhancers	H9 Cell Line	embryonic stem cell
14	chr5:118787600-118787800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:118787600-118787800	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr5:118787600-118787800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
17	chr5:118787600-118787800	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr5:118787600-118787800	Enhancers	Primary T cells from cord blood	blood
19	chr5:118787600-118787800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
20	chr5:118787600-118787800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr5:118787600-118787800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr5:118787600-118787800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr5:118787600-118787800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr5:118787600-118787800	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr5:118787600-118787800	Weak transcription	Adipose Nuclei	Adipose
26	chr5:118787600-118787800	Enhancers	Brain Germinal Matrix	brain
27	chr5:118787600-118787800	Enhancers	Fetal Thymus	thymus
28	chr5:118787600-118787800	Flanking Active TSS	A549	lung
29	chr5:118787600-118787800	Enhancers	GM12878-XiMat	blood
30	chr5:118787600-118787800	ZNF genes & repeats	K562	blood
31	chr5:118787600-118788000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
32	chr5:118787600-118788000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr5:118787600-118788000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr5:118787600-118788000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr5:118787600-118788000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
36	chr5:118787600-118788000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr5:118787600-118788000	Flanking Active TSS	Liver	Liver
38	chr5:118787600-118788000	Flanking Active TSS	Colon Smooth Muscle	Colon
39	chr5:118787600-118788000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
40	chr5:118787600-118788000	Flanking Active TSS	Stomach Smooth Muscle	stomach
41	chr5:118787600-118788000	Enhancers	Spleen	Spleen
42	chr5:118787600-118788000	Flanking Active TSS	Hela-S3	cervix
43	chr5:118787600-118788000	Flanking Active TSS	HepG2	liver
44	chr5:118787600-118788000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
45	chr5:118787600-118788200	Weak transcription	Lung	lung
46	chr5:118787600-118788800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr5:118787600-118788800	Active TSS	Primary hematopoietic stem cells short term culture	blood
48	chr5:118787600-118788800	Active TSS	Brain Cingulate Gyrus	brain
49	chr5:118787600-118789000	Active TSS	Brain Angular Gyrus	brain
50	chr5:118787600-118789000	Active TSS	Fetal Heart	heart

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