Variant report

Variant	rs13080057
Chromosome Location	chr3:98502553-98502554
allele	A/G
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	MAZ	chr3:98502256-98502750	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:98502527-98502555	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:98500239-98520630	U87	brain:	n/a	n/a
4	POLR2A	chr3:98500581-98518912	U87	brain:	n/a	n/a
5	POLR2A	chr3:98500433-98518912	U87	brain:	n/a	n/a

Variant related genes	Relation type
ST3GAL6	TF binding region

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10428160	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10589669	0.85[EUR][1000 genomes]
rs11552978	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12107272	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12108018	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12108142	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13059624	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13065136	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13068317	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13072410	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13074614	0.87[EUR][1000 genomes]
rs13074787	0.81[EUR][1000 genomes]
rs13076960	0.87[EUR][1000 genomes]
rs13078549	0.81[EUR][1000 genomes]
rs13081992	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13083238	0.87[EUR][1000 genomes]
rs13083613	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13083934	0.87[EUR][1000 genomes]
rs13084692	0.87[EUR][1000 genomes]
rs13087627	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13087631	0.87[EUR][1000 genomes]
rs13088532	0.80[AMR][1000 genomes]
rs13091170	0.85[EUR][1000 genomes]
rs13091236	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13093128	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13096085	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13097876	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13100915	0.84[EUR][1000 genomes]
rs13100937	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34008360	0.87[EUR][1000 genomes]
rs34269725	0.84[EUR][1000 genomes]
rs34279227	0.87[EUR][1000 genomes]
rs34284740	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34394867	0.91[AMR][1000 genomes]
rs34428696	0.83[EUR][1000 genomes]
rs34470469	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34489202	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34688367	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34711372	0.87[EUR][1000 genomes]
rs34725039	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34826460	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34848749	0.87[EUR][1000 genomes]
rs34860591	0.89[EUR][1000 genomes]
rs34951301	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs35006699	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35025156	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35076733	0.85[EUR][1000 genomes]
rs35098355	0.87[EUR][1000 genomes]
rs35103318	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35219252	0.87[EUR][1000 genomes]
rs35234681	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35239055	0.87[EUR][1000 genomes]
rs35312318	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35366262	0.87[EUR][1000 genomes]
rs35422064	0.87[EUR][1000 genomes]
rs35499232	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35514544	0.84[EUR][1000 genomes]
rs35526367	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35539438	0.89[EUR][1000 genomes]
rs35764973	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35914268	0.87[EUR][1000 genomes]
rs35947806	0.87[EUR][1000 genomes]
rs36032715	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36098932	0.84[EUR][1000 genomes]
rs36157152	0.84[EUR][1000 genomes]
rs36175276	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs41267851	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55644421	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56083233	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56094988	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56246599	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56408882	0.91[AMR][1000 genomes]
rs6764579	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6805362	0.87[EUR][1000 genomes]
rs71311393	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71311394	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71311397	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71311398	0.87[EUR][1000 genomes]
rs71311402	0.87[EUR][1000 genomes]
rs71313504	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs71313508	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71313509	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71313510	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71313511	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7614053	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98478800-98515200	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr3:98483000-98517600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:98483200-98518000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr3:98483600-98513600	Weak transcription	Brain Germinal Matrix	brain
5	chr3:98483800-98515000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr3:98484000-98514000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr3:98484200-98515200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr3:98484800-98529800	Weak transcription	Primary B cells from cord blood	blood
9	chr3:98489800-98503000	Weak transcription	Psoas Muscle	Psoas
10	chr3:98490200-98525200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr3:98492200-98517800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:98494600-98506000	Enhancers	Aorta	Aorta
13	chr3:98496600-98503800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:98496800-98502800	Weak transcription	Fetal Thymus	thymus
15	chr3:98497000-98524600	Weak transcription	Fetal Brain Male	brain
16	chr3:98497400-98503600	Enhancers	Placenta	Placenta
17	chr3:98497800-98517200	Weak transcription	Fetal Brain Female	brain
18	chr3:98498000-98503000	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr3:98498000-98516600	Weak transcription	Stomach Mucosa	stomach
20	chr3:98498200-98505400	Strong transcription	Thymus	Thymus
21	chr3:98498400-98504600	Weak transcription	Fetal Intestine Small	intestine
22	chr3:98498600-98503000	Weak transcription	Right Atrium	heart
23	chr3:98498800-98506800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr3:98498800-98512800	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr3:98499000-98503000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:98499000-98503000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr3:98499000-98504200	Weak transcription	HSMM	muscle
28	chr3:98499200-98503200	Weak transcription	NHDF-Ad	bronchial
29	chr3:98499200-98503400	Weak transcription	NHLF	lung
30	chr3:98499200-98504200	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr3:98499200-98504600	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr3:98499200-98516600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr3:98499400-98503000	Weak transcription	Fetal Heart	heart
34	chr3:98499400-98503600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr3:98499400-98506400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr3:98499600-98503000	Weak transcription	Adipose Nuclei	Adipose
37	chr3:98499600-98507800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr3:98499600-98516600	Weak transcription	Brain Angular Gyrus	brain
39	chr3:98499800-98502800	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr3:98499800-98503200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:98499800-98514800	Weak transcription	Dnd41	blood
42	chr3:98500200-98506000	Enhancers	HMEC	breast
43	chr3:98500600-98502800	Strong transcription	Primary hematopoietic stem cells	blood
44	chr3:98500600-98504400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr3:98500800-98502800	Weak transcription	Pancreas	Pancrea
46	chr3:98500800-98505600	Genic enhancers	Monocytes-CD14+_RO01746	blood
47	chr3:98501000-98506600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr3:98501000-98507400	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr3:98501200-98503400	Genic enhancers	HUVEC	blood vessel
50	chr3:98501200-98504400	Weak transcription	Brain Hippocampus Middle	brain

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