Variant report

Variant	rs13005005
Chromosome Location	chr2:177717690-177717691
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:28)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:28 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr2:177717655-177717716	NHEK	skin:	n/a	n/a
2	CTCF	chr2:177717540-177717690	HMEC	breast:	n/a	n/a
3	CTCF	chr2:177717624-177717746	LNCaP	prostate:	n/a	n/a
4	CTCF	chr2:177717600-177717750	BE2_C	brain:	n/a	n/a
5	CTCF	chr2:177717640-177717790	GM12873	blood:	n/a	n/a
6	CTCF	chr2:177717620-177717770	HCT-116	colon:	n/a	n/a
7	CTCF	chr2:177717611-177717759	MCF-7	breast:	n/a	n/a
8	FOXA1	chr2:177717482-177717754	T-47D	breast:	n/a	n/a
9	CTCF	chr2:177717509-177717813	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTCF	chr2:177717560-177717710	HEK293	kidney:	n/a	n/a
11	JUND	chr2:177717419-177717746	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTCF	chr2:177717620-177717770	MCF-7	breast:	n/a	n/a
13	EP300	chr2:177717355-177717709	GM12878	blood:	n/a	chr2:177717501-177717510
14	RAD21	chr2:177717414-177717959	MCF-7	breast:	n/a	n/a
15	FOXA1	chr2:177717537-177717774	T-47D	breast:	n/a	n/a
16	CTCF	chr2:177717660-177717810	SK-N-SH_RA	brain:	n/a	n/a
17	CTCF	chr2:177717597-177717776	MCF-7	breast:	n/a	n/a
18	CTCF	chr2:177717600-177717750	HEEpiC	esophagus:	n/a	n/a
19	ZNF143	chr2:177717425-177717720	H1-hESC	embryonic stem cell:	n/a	n/a
20	CTCF	chr2:177717580-177717730	GM12871	blood:	n/a	n/a
21	CTCF	chr2:177717620-177717770	Caco-2	colon:	n/a	n/a
22	RAD21	chr2:177717475-177717856	H1-hESC	embryonic stem cell:	n/a	n/a
23	RAD21	chr2:177717305-177717911	H1-hESC	embryonic stem cell:	n/a	n/a
24	CTCF	chr2:177717625-177717726	H1-hESC	embryonic stem cell:	n/a	n/a
25	CTCF	chr2:177717644-177717778	LNCaP	prostate:	n/a	n/a
26	RAD21	chr2:177717481-177717865	H1-hESC	embryonic stem cell:	n/a	n/a
27	CTCF	chr2:177717600-177717750	HMEC	breast:	n/a	n/a
28	CTCF	chr2:177717620-177717770	GM12875	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:177709383..177714584-chr2:177715247..177719528,6	K562	blood:
2	chr2:177681843..177682647-chr2:177717606..177718164,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000227098	TF binding region
ENSG00000227098	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10930765	1.00[JPT][hapmap]
rs10930767	1.00[JPT][hapmap]
rs12469347	1.00[JPT][hapmap]
rs12469859	0.81[ASN][1000 genomes]
rs12614055	0.81[ASN][1000 genomes]
rs12615378	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12616782	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13421731	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1344900	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1355845	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1398968	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1513870	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1561278	0.81[ASN][1000 genomes]
rs16864736	1.00[JPT][hapmap]
rs17626597	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17627058	0.81[ASN][1000 genomes]
rs17628074	1.00[JPT][hapmap]
rs17679370	1.00[JPT][hapmap]
rs1866134	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2028186	0.85[ASN][1000 genomes]
rs2028187	0.85[ASN][1000 genomes]
rs4145341	0.81[ASN][1000 genomes]
rs56159313	0.81[ASN][1000 genomes]
rs56879349	0.81[ASN][1000 genomes]
rs6707899	1.00[JPT][hapmap]
rs6760271	1.00[JPT][hapmap]
rs714080	0.81[ASN][1000 genomes]
rs7588841	1.00[JPT][hapmap]
rs840698	1.00[JPT][hapmap]
rs840699	1.00[JPT][hapmap]
rs961425	0.81[ASN][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	nsv459953	chr2:177704321-177720675	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv583687	chr2:177704321-177720675	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv3050	chr2:177713430-177760533	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13005005	OLA1	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:177715600-177718000	Enhancers	iPS-18 Cell Line	embryonic stem cell
2	chr2:177715800-177722800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr2:177716000-177717800	Enhancers	Brain Germinal Matrix	brain
4	chr2:177716200-177718000	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr2:177716200-177722400	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr2:177716400-177719000	Enhancers	Primary T cells from cord blood	blood
7	chr2:177716600-177717800	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr2:177716600-177717800	Enhancers	Fetal Thymus	thymus
9	chr2:177716600-177718000	Enhancers	Thymus	Thymus
10	chr2:177716600-177722200	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr2:177716600-177722600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr2:177716600-177722600	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr2:177716600-177722800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr2:177716800-177718000	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr2:177716800-177718000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr2:177716800-177718200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr2:177716800-177721400	Weak transcription	Fetal Kidney	kidney
18	chr2:177717000-177717800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr2:177717000-177717800	Enhancers	Dnd41	blood
20	chr2:177717000-177718000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr2:177717200-177717800	Enhancers	H9 Cell Line	embryonic stem cell
22	chr2:177717200-177717800	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr2:177717200-177717800	Enhancers	Primary hematopoietic stem cells	blood
24	chr2:177717200-177718000	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr2:177717400-177717800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr2:177717400-177717800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr2:177717400-177717800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr2:177717400-177717800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
29	chr2:177717400-177717800	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr2:177717400-177718000	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr2:177717600-177717800	Enhancers	Small Intestine	intestine
32	chr2:177717600-177718800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr2:177717600-177719400	Enhancers	Primary T cells fromperipheralblood	blood

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