Variant report

Variant	rs62625035
Chromosome Location	chr10:97516401-97516402
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:97509445..97513285-chr10:97516260..97519488,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TCTN3-1	chr10:97512963-97516471	ENSG00000226688.1
2	lnc-TCTN3-1	chr10:97512963-97516471	NONHSAT015766

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10882623	0.87[EUR][1000 genomes]
rs10882624	0.87[EUR][1000 genomes]
rs10882626	0.87[EUR][1000 genomes]
rs10882627	0.87[EUR][1000 genomes]
rs10882628	0.87[EUR][1000 genomes]
rs10882629	0.87[EUR][1000 genomes]
rs10882630	0.87[EUR][1000 genomes]
rs10882631	0.87[EUR][1000 genomes]
rs10882632	0.87[EUR][1000 genomes]
rs10882633	0.85[EUR][1000 genomes]
rs10882634	0.87[EUR][1000 genomes]
rs10882635	0.85[EUR][1000 genomes]
rs11188366	0.87[EUR][1000 genomes]
rs11188368	0.87[EUR][1000 genomes]
rs11188369	0.87[EUR][1000 genomes]
rs11188370	0.87[EUR][1000 genomes]
rs11188371	0.87[EUR][1000 genomes]
rs11188376	0.87[EUR][1000 genomes]
rs11541780	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11542152	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12218873	0.87[EUR][1000 genomes]
rs12242866	0.87[EUR][1000 genomes]
rs12242918	0.87[EUR][1000 genomes]
rs12242923	0.87[EUR][1000 genomes]
rs12248661	0.87[EUR][1000 genomes]
rs12250514	0.87[EUR][1000 genomes]
rs12255572	0.87[EUR][1000 genomes]
rs3176887	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3176892	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3176893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3181116	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3181118	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3181125	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3181127	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35168849	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41291572	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7073436	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7084606	0.87[EUR][1000 genomes]
rs7086374	0.82[EUR][1000 genomes]
rs7097236	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7099430	0.87[EUR][1000 genomes]
rs7099515	0.87[EUR][1000 genomes]
rs7101227	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73325155	0.87[EUR][1000 genomes]
rs73325195	0.87[EUR][1000 genomes]
rs74150947	0.87[EUR][1000 genomes]
rs7896068	0.87[EUR][1000 genomes]
rs7900437	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7903143	0.85[EUR][1000 genomes]
rs7915682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7919673	0.92[AMR][1000 genomes];1.00[EUR][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	nsv531923	chr10:97366055-97725757	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv895905	chr10:97513362-97686064	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv895906	chr10:97513362-97703650	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62625035	TCTN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97514600-97516800	Active TSS	Primary hematopoietic stem cells	blood
2	chr10:97515000-97516600	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr10:97515000-97518200	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr10:97515000-97518400	Active TSS	Stomach Smooth Muscle	stomach
5	chr10:97515200-97516600	Active TSS	H9 Cell Line	embryonic stem cell
6	chr10:97515200-97516600	Active TSS	Psoas Muscle	Psoas
7	chr10:97515200-97516600	Weak transcription	Small Intestine	intestine
8	chr10:97515200-97516800	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr10:97515200-97516800	Active TSS	Brain Cingulate Gyrus	brain
10	chr10:97515200-97517000	Active TSS	Fetal Intestine Small	intestine
11	chr10:97515200-97517400	Active TSS	Brain Anterior Caudate	brain
12	chr10:97515200-97517400	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr10:97515200-97517600	Active TSS	Colonic Mucosa	Colon
14	chr10:97515200-97518200	Active TSS	Duodenum Mucosa	Duodenum
15	chr10:97515200-97518200	Active TSS	GM12878-XiMat	blood
16	chr10:97515200-97518400	Active TSS	Brain Hippocampus Middle	brain
17	chr10:97515200-97518600	Active TSS	Rectal Mucosa Donor 29	rectum
18	chr10:97515400-97516600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr10:97515400-97516600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr10:97515400-97516600	Active TSS	Fetal Stomach	stomach
21	chr10:97515400-97516600	Active TSS	Ovary	ovary
22	chr10:97515400-97516600	Active TSS	Right Ventricle	heart
23	chr10:97515400-97516800	Active TSS	H1 Cell Line	embryonic stem cell
24	chr10:97515400-97516800	Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr10:97515400-97516800	Active TSS	Rectal Smooth Muscle	rectum
26	chr10:97515400-97517000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr10:97515400-97517000	Active TSS	Colon Smooth Muscle	Colon
28	chr10:97515400-97517000	Active TSS	Rectal Mucosa Donor 31	rectum
29	chr10:97515400-97517000	Flanking Active TSS	HUVEC	blood vessel
30	chr10:97515400-97517200	Active TSS	Adipose Nuclei	Adipose
31	chr10:97515400-97517200	Active TSS	Aorta	Aorta
32	chr10:97515400-97517200	Active TSS	Brain Substantia Nigra	brain
33	chr10:97515400-97517200	Active TSS	Right Atrium	heart
34	chr10:97515400-97517400	Active TSS	Fetal Intestine Large	intestine
35	chr10:97515400-97517400	Active TSS	Skeletal Muscle Female	skeletal muscle
36	chr10:97515400-97517600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
37	chr10:97515400-97517600	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr10:97515400-97518200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr10:97515600-97516600	Active TSS	iPS-20b Cell Line	embryonic stem cell
40	chr10:97515600-97516600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr10:97515600-97516600	Enhancers	Fetal Lung	lung
42	chr10:97515600-97516800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr10:97515600-97516800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr10:97515600-97516800	Active TSS	Left Ventricle	heart
45	chr10:97515600-97517000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr10:97515600-97517000	Active TSS	Fetal Kidney	kidney
47	chr10:97515600-97517000	Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr10:97515600-97517200	Active TSS	Brain Angular Gyrus	brain
49	chr10:97515600-97517200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
50	chr10:97515600-97517200	Active TSS	Fetal Muscle Leg	muscle

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