Variant report

Variant	rs13385999
Chromosome Location	chr2:55191897-55191898
allele	G/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	POLR2A	chr2:55191535-55192815	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr2:55190471-55199022	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr2:55190362-55199062	U87	brain:	n/a	n/a
4	POLR2A	chr2:55191336-55197109	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr2:55190420-55192555	IMR90	lung:	n/a	n/a
6	POLR2A	chr2:55190362-55199105	U87	brain:	n/a	n/a
7	POLR2A	chr2:55190452-55192054	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55130491..55133378-chr2:55191719..55193881,2	MCF-7	breast:

Variant related genes	Relation type
EML6	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10084445	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10170102	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10173203	0.86[LWK][hapmap]
rs10175952	1.00[CEU][hapmap];0.86[AMR][1000 genomes]
rs10179491	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10180207	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10181115	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10191684	0.92[AMR][1000 genomes]
rs10191748	0.82[AMR][1000 genomes]
rs10197533	1.00[CEU][hapmap];0.87[GIH][hapmap];0.82[AMR][1000 genomes]
rs10198096	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10207701	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11125554	1.00[CEU][hapmap];0.84[AMR][1000 genomes]
rs13387710	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13394823	0.92[AMR][1000 genomes]
rs13394824	0.92[AMR][1000 genomes]
rs13400353	1.00[CEU][hapmap]
rs17046567	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17046569	1.00[CEU][hapmap];0.90[GIH][hapmap];0.88[LWK][hapmap];0.82[TSI][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3198123	0.88[LWK][hapmap]
rs4358163	1.00[CEU][hapmap];0.85[GIH][hapmap];0.81[EUR][1000 genomes]
rs60989108	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6715980	1.00[CEU][hapmap];0.90[GIH][hapmap];0.81[EUR][1000 genomes]
rs6725187	0.81[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6758258	0.90[TSI][hapmap]
rs72912579	0.86[AMR][1000 genomes]
rs7570298	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7584992	1.00[ASW][hapmap];0.86[GIH][hapmap];0.91[LWK][hapmap];0.91[MKK][hapmap];0.90[TSI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[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	nsv582029	chr2:55159043-55204498	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55168800-55193400	Weak transcription	Primary B cells from peripheral blood	blood
2	chr2:55173000-55193400	Weak transcription	Aorta	Aorta
3	chr2:55173200-55203400	Weak transcription	Gastric	stomach
4	chr2:55173600-55194000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr2:55173600-55195000	Weak transcription	Pancreas	Pancrea
6	chr2:55174800-55194000	Weak transcription	Brain Germinal Matrix	brain
7	chr2:55175400-55193200	Weak transcription	Fetal Brain Female	brain
8	chr2:55175600-55194600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr2:55175800-55193800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr2:55177800-55193800	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr2:55178200-55193400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr2:55178600-55193400	Weak transcription	Spleen	Spleen
13	chr2:55180600-55193600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr2:55180600-55195400	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr2:55180600-55196000	Weak transcription	NH-A	brain
16	chr2:55181600-55193600	Weak transcription	Lung	lung
17	chr2:55181600-55203400	Weak transcription	Ovary	ovary
18	chr2:55183000-55192000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr2:55183200-55193200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr2:55183200-55193200	Weak transcription	NHLF	lung
21	chr2:55183200-55206800	Weak transcription	Stomach Mucosa	stomach
22	chr2:55183400-55196600	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr2:55183800-55193600	Weak transcription	A549	lung
24	chr2:55184000-55192200	Weak transcription	Fetal Stomach	stomach
25	chr2:55184800-55192400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr2:55184800-55195800	Weak transcription	Thymus	Thymus
27	chr2:55184800-55214800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr2:55185000-55192800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr2:55185200-55193400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr2:55185200-55194000	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr2:55186000-55194400	Weak transcription	Primary B cells from cord blood	blood
32	chr2:55186400-55193400	Weak transcription	Brain Anterior Caudate	brain
33	chr2:55186400-55193800	Weak transcription	Brain Angular Gyrus	brain
34	chr2:55186600-55192400	Weak transcription	K562	blood
35	chr2:55187000-55195000	Weak transcription	Dnd41	blood
36	chr2:55187600-55194200	Weak transcription	Brain Cingulate Gyrus	brain
37	chr2:55188200-55193000	Weak transcription	Brain Hippocampus Middle	brain
38	chr2:55189600-55192400	Enhancers	HSMMtube	muscle
39	chr2:55190000-55193400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr2:55190000-55198400	Weak transcription	Colonic Mucosa	Colon
41	chr2:55190000-55203400	Weak transcription	Small Intestine	intestine
42	chr2:55190400-55192600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:55190400-55194400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr2:55190600-55192400	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr2:55190600-55193400	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr2:55190600-55193600	Enhancers	Primary hematopoietic stem cells	blood
47	chr2:55190600-55198000	Genic enhancers	Fetal Muscle Leg	muscle
48	chr2:55190800-55194400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr2:55190800-55194400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
50	chr2:55190800-55196600	Weak transcription	Rectal Mucosa Donor 29	rectum

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