Variant report

Variant	rs2560275
Chromosome Location	chr5:94889434-94889435
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	MAX	chr5:94889419-94889760	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr5:94889417-94891124	K562	blood:	n/a	n/a
3	MAFK	chr5:94889409-94892087	Hela-S3	cervix:	n/a	chr5:94890316-94890327 chr5:94891579-94891588 chr5:94891579-94891589
4	CEBPB	chr5:94889410-94889828	Hela-S3	cervix:	n/a	n/a
5	MAX	chr5:94889409-94889692	K562	blood:	n/a	n/a
6	BHLHE40	chr5:94889422-94889832	K562	blood:	n/a	n/a
7	GATA3	chr5:94889392-94889888	MCF-7	breast:	n/a	n/a
8	MXI1	chr5:94889414-94891980	IMR90	lung:	n/a	n/a
9	RCOR1	chr5:94889373-94889849	K562	blood:	n/a	n/a
10	TEAD4	chr5:94889338-94889952	K562	blood:	n/a	n/a
11	RPC155	chr5:94889149-94889731	Hela-S3	cervix:	n/a	n/a
12	GATA3	chr5:94889202-94890043	MCF-7	breast:	n/a	chr5:94889213-94889224
13	GTF3C2	chr5:94889255-94889690	K562	blood:	n/a	n/a
14	GATA3	chr5:94889399-94889790	T-47D	breast:	n/a	n/a
15	CCNT2	chr5:94889430-94889659	K562	blood:	n/a	n/a
16	GATA3	chr5:94889423-94889762	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:94888891..94893786-chr5:94981389..94987516,11	K562	blood:
2	chr5:94877399..94880074-chr5:94889020..94891541,2	MCF-7	breast:
3	chr5:94885448..94888187-chr5:94888844..94890737,5	K562	blood:
4	chr5:94889331..94891668-chr5:96036859..96038572,2	K562	blood:

Variant related genes	Relation type
ARSK	TF binding region
TTC37	TF binding region
ENSG00000198677	Chromatin interaction
ENSG00000175449	Chromatin interaction
ENSG00000153113	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10040106	1.00[YRI][hapmap]
rs1123965	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1162859	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13162779	0.95[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2059786	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2545842	1.00[YRI][hapmap]
rs2560256	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2560276	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2560277	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2731816	0.92[YRI][hapmap]
rs2731818	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2731828	0.82[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2731838	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4573018	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6556871	0.90[CHB][hapmap];0.85[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882388	chr5:94764006-94925849	Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2560275	TTC37	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:94827200-94889600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:94847400-94890000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:94849200-94890000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr5:94853800-94890000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:94865200-94890000	Weak transcription	Aorta	Aorta
6	chr5:94877600-94889600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr5:94879600-94889600	Weak transcription	Fetal Intestine Small	intestine
8	chr5:94881000-94889600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr5:94881400-94889600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr5:94881600-94889600	Weak transcription	Thymus	Thymus
11	chr5:94882400-94889600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr5:94882400-94889600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:94882400-94889600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr5:94882400-94889600	Weak transcription	Fetal Stomach	stomach
15	chr5:94883000-94889600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr5:94883000-94889600	Weak transcription	Left Ventricle	heart
17	chr5:94883000-94889600	Weak transcription	HSMMtube	muscle
18	chr5:94883000-94890000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr5:94883200-94889600	Weak transcription	Fetal Muscle Leg	muscle
20	chr5:94883200-94889600	Weak transcription	Ovary	ovary
21	chr5:94883600-94889600	Weak transcription	A549	lung
22	chr5:94885200-94889600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr5:94885200-94889600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr5:94885400-94889600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr5:94886000-94889600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr5:94886000-94889600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr5:94886000-94889600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr5:94886400-94889600	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr5:94887000-94889600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr5:94887000-94889600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr5:94887000-94889600	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr5:94887000-94889800	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr5:94887200-94890000	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr5:94887400-94889600	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr5:94887600-94889600	Weak transcription	Fetal Heart	heart
36	chr5:94887600-94889600	Weak transcription	Psoas Muscle	Psoas
37	chr5:94887800-94890000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr5:94888000-94890000	Weak transcription	Small Intestine	intestine
39	chr5:94888600-94889800	Enhancers	Placenta Amnion	Placenta Amnion
40	chr5:94888800-94889600	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr5:94888800-94889600	Weak transcription	Brain Angular Gyrus	brain
42	chr5:94888800-94889600	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr5:94888800-94889600	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr5:94889000-94889600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr5:94889000-94889600	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr5:94889000-94889600	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr5:94889000-94889600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr5:94889000-94889600	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr5:94889000-94889600	Weak transcription	Brain Germinal Matrix	brain
50	chr5:94889000-94890000	Weak transcription	Fetal Muscle Trunk	muscle

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