Variant report

Variant	rs6884349
Chromosome Location	chr5:43298430-43298431
allele	C/T
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	GATA3	chr5:43298405-43299082	SH-SY5Y	brain:	n/a	n/a
2	POLR2A	chr5:43297959-43299477	K562	blood:	n/a	n/a
3	POLR2A	chr5:43297999-43299179	HepG2	liver:	n/a	n/a
4	POLR2A	chr5:43298022-43299178	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:43296533..43300928-chr5:43302565..43304605,4	K562	blood:
2	chr5:43296533..43300517-chr5:43302565..43304936,4	K562	blood:
3	chr5:43293726..43296499-chr5:43296794..43299254,2	MCF-7	breast:

Variant related genes	Relation type
HMGCS1	TF binding region
ENSG00000112972	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10037409	0.86[EUR][1000 genomes]
rs10037706	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap]
rs10038859	0.86[EUR][1000 genomes]
rs10040897	0.86[EUR][1000 genomes]
rs10043148	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10052384	0.86[EUR][1000 genomes]
rs10054415	1.00[CEU][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10056437	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10062031	0.86[EUR][1000 genomes]
rs10062121	0.86[EUR][1000 genomes]
rs10062598	1.00[CEU][hapmap];0.83[YRI][hapmap];0.86[EUR][1000 genomes]
rs10064967	0.86[EUR][1000 genomes]
rs10067763	1.00[CEU][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10069507	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap]
rs10077324	1.00[EUR][1000 genomes]
rs10079530	1.00[EUR][1000 genomes]
rs10473306	1.00[CEU][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10473308	1.00[CEU][hapmap];0.95[YRI][hapmap];0.86[EUR][1000 genomes]
rs11955467	1.00[EUR][1000 genomes]
rs1478436	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16874093	1.00[CEU][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16874094	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs28450849	0.86[EUR][1000 genomes]
rs28608156	1.00[EUR][1000 genomes]
rs28856961	0.86[EUR][1000 genomes]
rs4326149	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs55645370	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60520238	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6865440	1.00[GIH][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.86[EUR][1000 genomes]
rs6887169	1.00[MEX][hapmap]
rs6892413	0.86[EUR][1000 genomes]
rs6893898	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6894240	1.00[CEU][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes]
rs6895237	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap]
rs7356654	0.86[EUR][1000 genomes]
rs7356727	0.81[AFR][1000 genomes]
rs73751075	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73751078	0.86[EUR][1000 genomes]
rs73751082	0.86[EUR][1000 genomes]
rs73751083	0.86[EUR][1000 genomes]
rs7710717	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7715267	1.00[EUR][1000 genomes]
rs7729140	1.00[CEU][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7729145	1.00[CEU][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7733732	1.00[CEU][hapmap];0.83[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9292869	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9292870	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9292872	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9292875	1.00[CEU][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
2	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
3	nsv508352	chr5:43237830-43391062	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43284200-43309400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:43285000-43300800	Strong transcription	Cortex derived primary cultured neurospheres	brain
3	chr5:43285600-43300000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr5:43285600-43302000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr5:43285600-43302800	Strong transcription	Duodenum Mucosa	Duodenum
6	chr5:43286200-43300600	Strong transcription	Fetal Intestine Large	intestine
7	chr5:43286400-43302200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr5:43286400-43302400	Strong transcription	GM12878-XiMat	blood
9	chr5:43286600-43300400	Strong transcription	Fetal Thymus	thymus
10	chr5:43286600-43300800	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr5:43286600-43301000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr5:43286600-43301400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr5:43286600-43303000	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr5:43286600-43303000	Strong transcription	Primary hematopoietic stem cells	blood
15	chr5:43286800-43300000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr5:43286800-43300400	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr5:43286800-43300400	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr5:43286800-43301000	Strong transcription	K562	blood
19	chr5:43286800-43301400	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr5:43286800-43301800	Strong transcription	HMEC	breast
21	chr5:43286800-43302400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr5:43286800-43302600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr5:43286800-43302600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr5:43286800-43304400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr5:43287000-43302800	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr5:43287000-43305000	Strong transcription	HUVEC	blood vessel
27	chr5:43287200-43301000	Strong transcription	Primary B cells from peripheral blood	blood
28	chr5:43287400-43298600	Weak transcription	Right Ventricle	heart
29	chr5:43287400-43300800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr5:43287400-43302600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr5:43287400-43302800	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr5:43287600-43302000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr5:43287800-43298800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr5:43287800-43299400	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr5:43287800-43300600	Strong transcription	HepG2	liver
36	chr5:43287800-43303600	Strong transcription	H9 Cell Line	embryonic stem cell
37	chr5:43288200-43312400	Weak transcription	Spleen	Spleen
38	chr5:43288600-43310000	Weak transcription	Aorta	Aorta
39	chr5:43288800-43303600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr5:43289600-43303800	Strong transcription	Primary B cells from cord blood	blood
41	chr5:43289800-43300800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr5:43290200-43298800	Strong transcription	Colon Smooth Muscle	Colon
43	chr5:43290400-43298800	Strong transcription	Brain Germinal Matrix	brain
44	chr5:43290400-43299200	Strong transcription	Fetal Brain Female	brain
45	chr5:43290400-43299200	Strong transcription	Fetal Lung	lung
46	chr5:43290400-43302400	Strong transcription	Primary T cells from cord blood	blood
47	chr5:43290600-43298800	Strong transcription	Brain Anterior Caudate	brain
48	chr5:43290600-43298800	Strong transcription	Brain Cingulate Gyrus	brain
49	chr5:43290600-43299400	Strong transcription	Placenta	Placenta
50	chr5:43290600-43299400	Strong transcription	HSMM	muscle

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