Variant report

Variant	rs72934641
Chromosome Location	chr3:98520339-98520340
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ST3GAL6-3	chr3:98520293-98520461	NONHSAT147244

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10084679	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12330381	0.85[AMR][1000 genomes]
rs13317610	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs13318960	0.85[AMR][1000 genomes]
rs13320266	0.83[ASN][1000 genomes]
rs13320890	0.94[EUR][1000 genomes]
rs13322253	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28417568	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28429424	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28489284	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28528154	0.85[AMR][1000 genomes]
rs28650813	0.85[AMR][1000 genomes]
rs3796133	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56172805	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs59906228	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72932691	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72932700	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72934623	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9289699	0.85[AMR][1000 genomes]
rs9289700	0.85[AMR][1000 genomes]
rs9810407	0.83[ASN][1000 genomes]
rs9812438	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9818215	0.83[ASN][1000 genomes]
rs9833945	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9836437	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs9836915	0.83[ASN][1000 genomes]
rs9838166	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs9838238	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9838706	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9839559	1.00[EUR][1000 genomes]
rs9848335	0.85[AMR][1000 genomes]
rs9848583	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9862660	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9870500	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9870940	0.85[AMR][1000 genomes]
rs9879302	0.85[AMR][1000 genomes]
rs9883751	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv1009032	chr3:98514221-98607721	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98484800-98529800	Weak transcription	Primary B cells from cord blood	blood
2	chr3:98490200-98525200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr3:98497000-98524600	Weak transcription	Fetal Brain Male	brain
4	chr3:98502200-98523800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:98502400-98523800	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr3:98503400-98576400	Weak transcription	Gastric	stomach
7	chr3:98503600-98523800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr3:98504600-98534800	Weak transcription	Small Intestine	intestine
9	chr3:98505000-98525600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:98505400-98523800	Weak transcription	Pancreas	Pancrea
11	chr3:98505400-98524400	Weak transcription	Thymus	Thymus
12	chr3:98505800-98524600	Weak transcription	Psoas Muscle	Psoas
13	chr3:98506400-98524400	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr3:98506800-98523800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr3:98507800-98529000	Weak transcription	Brain Substantia Nigra	brain
16	chr3:98508000-98524600	Weak transcription	GM12878-XiMat	blood
17	chr3:98508200-98524600	Weak transcription	Fetal Heart	heart
18	chr3:98512200-98521000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:98512400-98520800	Strong transcription	Muscle Satellite Cultured Cells	--
20	chr3:98512800-98520400	Strong transcription	HSMM	muscle
21	chr3:98513000-98520800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:98513000-98524400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr3:98513400-98520600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr3:98513400-98520800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr3:98513400-98520800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr3:98513400-98523800	Weak transcription	Duodenum Mucosa	Duodenum
27	chr3:98513600-98520800	Strong transcription	NH-A	brain
28	chr3:98513600-98536600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr3:98513600-98539200	Weak transcription	Colonic Mucosa	Colon
30	chr3:98513800-98520600	Strong transcription	A549	lung
31	chr3:98513800-98520800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:98513800-98520800	Strong transcription	Osteobl	bone
33	chr3:98513800-98521000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr3:98513800-98524400	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr3:98513800-98525400	Weak transcription	Esophagus	oesophagus
36	chr3:98513800-98526000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr3:98514000-98520600	Strong transcription	NHDF-Ad	bronchial
38	chr3:98515000-98520400	Strong transcription	HUVEC	blood vessel
39	chr3:98515000-98520600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr3:98515000-98520600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr3:98515000-98520800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr3:98515200-98520600	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr3:98515400-98524400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr3:98515400-98524600	Weak transcription	Placenta	Placenta
45	chr3:98515600-98523800	Weak transcription	Aorta	Aorta
46	chr3:98515600-98523800	Weak transcription	Liver	Liver
47	chr3:98515600-98533400	Weak transcription	Fetal Intestine Small	intestine
48	chr3:98516400-98520800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr3:98516600-98520600	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr3:98516600-98520600	Genic enhancers	NHEK	skin

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