Variant report

Variant	rs9600553
Chromosome Location	chr13:76376730-76376731
allele	A/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	chr13:76376603-76376939	SK-N-SH	brain:	n/a	n/a
2	TCF12	chr13:76376320-76376795	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr13:76376630-76377001	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr13:76376698-76376840	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
LMO7	TF binding region

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

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs2273995	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs3783027	1.00[EUR][1000 genomes]
rs56915688	1.00[EUR][1000 genomes]
rs57908776	1.00[EUR][1000 genomes]
rs58875660	1.00[EUR][1000 genomes]
rs59762752	1.00[EUR][1000 genomes]
rs685938	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7324230	0.81[JPT][hapmap]
rs73542522	1.00[EUR][1000 genomes]
rs73542559	1.00[EUR][1000 genomes]
rs74096469	1.00[EUR][1000 genomes]
rs7995235	1.00[EUR][1000 genomes]
rs7998891	1.00[EUR][1000 genomes]
rs7999724	1.00[EUR][1000 genomes]
rs8001459	1.00[EUR][1000 genomes]
rs9318372	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9318374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9318375	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9593125	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9593126	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9593127	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9593128	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9600549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9600551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9600552	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv832646	chr13:76300428-76483102	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	esv2758333	chr13:76321610-76542003	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	esv2759950	chr13:76321610-76542003	Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76361600-76397800	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr13:76361800-76377400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr13:76362600-76377000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr13:76363000-76377000	Weak transcription	GM12878-XiMat	blood
5	chr13:76363200-76381800	Weak transcription	Fetal Stomach	stomach
6	chr13:76364600-76385000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr13:76366400-76380200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr13:76366800-76379400	Weak transcription	Pancreas	Pancrea
9	chr13:76366800-76379400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr13:76366800-76380200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr13:76366800-76380200	Weak transcription	Lung	lung
12	chr13:76367000-76377000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr13:76367000-76379800	Weak transcription	Brain Angular Gyrus	brain
14	chr13:76367000-76380200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr13:76367000-76387000	Weak transcription	Ovary	ovary
16	chr13:76367200-76377400	Weak transcription	Fetal Kidney	kidney
17	chr13:76367400-76377400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr13:76367400-76380600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr13:76367400-76384400	Weak transcription	Fetal Lung	lung
20	chr13:76369600-76377400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr13:76369800-76376800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr13:76370400-76415600	Weak transcription	Primary B cells from cord blood	blood
23	chr13:76370800-76378800	Genic enhancers	Osteobl	bone
24	chr13:76370800-76382400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr13:76371400-76379000	Weak transcription	Placenta	Placenta
26	chr13:76371600-76377000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr13:76371600-76377200	Weak transcription	Primary B cells from peripheral blood	blood
28	chr13:76371800-76377200	Enhancers	Fetal Heart	heart
29	chr13:76372000-76377200	Weak transcription	Small Intestine	intestine
30	chr13:76372000-76379600	Weak transcription	Colonic Mucosa	Colon
31	chr13:76372200-76376800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr13:76372200-76378400	Weak transcription	Fetal Muscle Leg	muscle
33	chr13:76372400-76380200	Weak transcription	Gastric	stomach
34	chr13:76373000-76376800	Weak transcription	HUVEC	blood vessel
35	chr13:76373000-76414600	Weak transcription	HMEC	breast
36	chr13:76373200-76377400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr13:76373200-76379000	Weak transcription	Fetal Muscle Trunk	muscle
38	chr13:76373200-76385800	Strong transcription	Hela-S3	cervix
39	chr13:76373400-76376800	Weak transcription	Right Ventricle	heart
40	chr13:76373400-76377400	Strong transcription	HSMMtube	muscle
41	chr13:76373400-76380800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr13:76373400-76387200	Weak transcription	Psoas Muscle	Psoas
43	chr13:76374000-76377000	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr13:76374400-76377200	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr13:76374400-76377600	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr13:76374400-76380200	Weak transcription	Rectal Smooth Muscle	rectum
47	chr13:76374600-76380400	Enhancers	iPS-18 Cell Line	embryonic stem cell
48	chr13:76374800-76377000	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr13:76374800-76377200	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr13:76374800-76377200	Strong transcription	Duodenum Mucosa	Duodenum

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