Variant report

Variant	rs17046594
Chromosome Location	chr2:55244538-55244539
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:55244499-55244640	ProgFib	skin:	n/a	n/a
2	POLR2A	chr2:55244445-55245266	U87	brain:	n/a	n/a
3	POLR2A	chr2:55244445-55245260	U87	brain:	n/a	n/a
4	POLR2A	chr2:55244385-55245194	U87	brain:	n/a	n/a
5	POLR2A	chr2:55241938-55261416	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:55243678..55249957-chr2:55274888..55279397,9	MCF-7	breast:
2	chr2:55242881..55244932-chr2:55247245..55249562,2	K562	blood:
3	chr2:55244120..55248820-chr2:55275882..55279343,5	K562	blood:
4	chr2:55243166..55246645-chr2:55249862..55254918,6	K562	blood:
5	chr2:55243006..55245333-chr2:55275948..55278441,2	MCF-7	breast:
6	chr2:55238560..55241765-chr2:55242966..55244949,3	K562	blood:
7	chr2:55239258..55241140-chr2:55243082..55244742,2	K562	blood:

No data

Variant related genes	Relation type
RNU6-433P	TF binding region
ENSG00000115310	Chromatin interaction
ENSG00000200086	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10189379	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10496036	0.96[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs12464447	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12464595	0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12475787	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12475904	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12479297	0.91[ASN][1000 genomes]
rs17046570	0.96[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17347089	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17418675	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2289747	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55659423	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55698303	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55993793	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56013263	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6545467	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6707036	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs67156582	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6730728	0.91[ASN][1000 genomes]
rs72795431	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72795440	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7582359	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs7584354	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7584386	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7601625	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs887	0.90[JPT][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834069	chr2:55096597-55251680	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv874155	chr2:55205262-55307646	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55203800-55258400	Weak transcription	Esophagus	oesophagus
2	chr2:55232200-55244800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:55234800-55244800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:55234800-55246000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:55237600-55246000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:55237600-55247800	Weak transcription	Left Ventricle	heart
7	chr2:55237600-55249600	Weak transcription	Gastric	stomach
8	chr2:55237600-55250200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr2:55237600-55258600	Weak transcription	Ovary	ovary
10	chr2:55237600-55272600	Weak transcription	Fetal Stomach	stomach
11	chr2:55238200-55245800	Weak transcription	Brain Germinal Matrix	brain
12	chr2:55238400-55244600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr2:55238400-55249200	Weak transcription	Pancreas	Pancrea
14	chr2:55238400-55249600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr2:55238400-55250800	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr2:55238400-55251200	Weak transcription	Psoas Muscle	Psoas
17	chr2:55238400-55252200	Weak transcription	Fetal Thymus	thymus
18	chr2:55238400-55252400	Weak transcription	Thymus	Thymus
19	chr2:55238400-55253200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:55239200-55244600	Weak transcription	Primary B cells from cord blood	blood
21	chr2:55239200-55244800	Weak transcription	Fetal Muscle Leg	muscle
22	chr2:55239200-55247800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr2:55239400-55244800	Enhancers	Muscle Satellite Cultured Cells	--
24	chr2:55239400-55245000	Weak transcription	Primary B cells from peripheral blood	blood
25	chr2:55240000-55244800	Weak transcription	Dnd41	blood
26	chr2:55240400-55244800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr2:55240400-55249200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr2:55240400-55249800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr2:55240600-55249000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr2:55240800-55249600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr2:55240800-55250200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr2:55241000-55244600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr2:55241000-55244600	Weak transcription	Primary hematopoietic stem cells	blood
34	chr2:55241000-55249000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr2:55241000-55249000	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr2:55241000-55249600	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr2:55241000-55272400	Weak transcription	Fetal Kidney	kidney
38	chr2:55241200-55244600	Weak transcription	Fetal Brain Female	brain
39	chr2:55241200-55245600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr2:55241200-55247400	Weak transcription	Fetal Intestine Large	intestine
41	chr2:55241200-55247800	Weak transcription	Fetal Intestine Small	intestine
42	chr2:55241200-55249000	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr2:55241200-55249200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr2:55241200-55249600	Weak transcription	Fetal Heart	heart
45	chr2:55241400-55246000	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr2:55241400-55249200	Weak transcription	Primary T cells from cord blood	blood
47	chr2:55241400-55253400	Weak transcription	Fetal Lung	lung
48	chr2:55241800-55244600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr2:55241800-55245000	Enhancers	HUVEC	blood vessel
50	chr2:55241800-55247800	Weak transcription	Lung	lung

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