Variant report

Variant	rs41291572
Chromosome Location	chr10:97453703-97453704
allele	A/C
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	PAX5	chr10:97453445-97454161	GM12878	blood:	n/a	n/a
2	EGR1	chr10:97453173-97454237	HCT-116	colon:	n/a	chr10:97453715-97453729 chr10:97453716-97453730 chr10:97453715-97453728 chr10:97453715-97453728 chr10:97453717-97453727 chr10:97453971-97453981 chr10:97453718-97453727 chr10:97454002-97454012 chr10:97453717-97453727 chr10:97453716-97453727
3	POLR2A	chr10:97453040-97454109	GM19099	blood:	n/a	n/a
4	MAX	chr10:97453502-97454071	K562	blood:	n/a	n/a
5	MAZ	chr10:97452966-97454230	IMR90	lung:	n/a	n/a
6	RUNX3	chr10:97453354-97454255	GM12878	blood:	n/a	n/a
7	MAX	chr10:97453385-97454240	MCF-7	breast:	n/a	n/a
8	NFATC1	chr10:97453483-97454195	GM12878	blood:	n/a	n/a
9	TAF1	chr10:97453403-97453749	GM12878	blood:	n/a	n/a
10	MAX	chr10:97453396-97454156	SK-N-SH	brain:	n/a	n/a
11	SP1	chr10:97453499-97454164	GM12878	blood:	n/a	chr10:97453758-97453779 chr10:97453799-97453820
12	POLR2A	chr10:97453048-97453987	Raji	blood:	n/a	n/a
13	POLR2A	chr10:97453344-97454198	PANC-1	pancreas:	n/a	n/a
14	POLR2A	chr10:97453439-97453859	K562	blood:	n/a	n/a
15	E2F4	chr10:97453647-97454005	GM12878	blood:	n/a	chr10:97453800-97453809
16	POLR2A	chr10:97453490-97453765	A549	lung:	n/a	n/a
17	MAX	chr10:97453540-97454064	H1-hESC	embryonic stem cell:	n/a	n/a
18	NFIC	chr10:97453340-97454144	ECC-1	luminal epithelium:	n/a	n/a
19	ZNF384	chr10:97453632-97454213	K562	blood:	n/a	n/a
20	MYC	chr10:97453485-97454065	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr10:97453104-97453989	GM12878	blood:	n/a	n/a
22	RCOR1	chr10:97453456-97454168	GM12878	blood:	n/a	n/a
23	MEF2A	chr10:97453694-97454225	GM12878	blood:	n/a	chr10:97454170-97454181
24	POLR2A	chr10:97453415-97454022	GM18526	blood:	n/a	n/a
25	POLR2A	chr10:97453301-97453927	MCF-7	breast:	n/a	n/a
26	ZMIZ1	chr10:97453593-97454043	K562	blood:	n/a	n/a
27	MYC	chr10:97453517-97453903	MCF-7	breast:	n/a	n/a
28	FOXP2	chr10:97453483-97454112	PFSK-1	brain:	n/a	n/a
29	MAX	chr10:97453183-97454160	ECC-1	luminal epithelium:	n/a	n/a
30	RAD21	chr10:97453640-97454239	MCF-7	breast:	n/a	chr10:97453931-97453950 chr10:97454003-97454016
31	POLR2A	chr10:97453410-97454021	GM18951	blood:	n/a	n/a
32	YY1	chr10:97453331-97453799	GM12892	blood:	n/a	n/a
33	SIN3AK20	chr10:97453334-97453752	A549	lung:	n/a	n/a
34	RFX5	chr10:97453129-97454205	Hela-S3	cervix:	n/a	chr10:97453885-97453901 chr10:97453888-97453902 chr10:97453768-97453777 chr10:97453886-97453899 chr10:97453890-97453899 chr10:97453886-97453900
35	ZKSCAN1	chr10:97453280-97454154	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr10:97453388-97453834	GM12878	blood:	n/a	n/a
37	CREB1	chr10:97453147-97454198	HepG2	liver:	n/a	n/a
38	YY1	chr10:97453310-97454142	ECC-1	luminal epithelium:	n/a	n/a
39	POLR2A	chr10:97453400-97453804	HepG2	liver:	n/a	n/a
40	FOXM1	chr10:97453216-97454333	ECC-1	luminal epithelium:	n/a	chr10:97454279-97454287
41	PAX5	chr10:97453466-97454119	GM12878	blood:	n/a	n/a
42	SIN3AK20	chr10:97453435-97454139	SK-N-SH	brain:	n/a	n/a
43	RAD21	chr10:97453635-97454267	A549	lung:	n/a	chr10:97453931-97453950 chr10:97454003-97454016
44	POLR2A	chr10:97452985-97454119	IMR90	lung:	n/a	n/a
45	POLR2A	chr10:97453279-97454151	H1-neurons	neurons:	n/a	n/a
46	SIN3AK20	chr10:97453327-97454051	HepG2	liver:	n/a	n/a
47	POLR2A	chr10:97453346-97453845	A549	lung:	n/a	n/a
48	NRF1	chr10:97453447-97454105	GM12878	blood:	n/a	chr10:97453649-97453660 chr10:97453867-97453876
49	CTCF	chr10:97453565-97454301	MCF-7	breast:	n/a	chr10:97453933-97453946 chr10:97453931-97453947 chr10:97453933-97453946 chr10:97453930-97453948 chr10:97453932-97453953
50	JUND	chr10:97453516-97454165	K562	blood:	n/a	chr10:97453767-97453776

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr10:97453674-97453724	Hela-S3	cervix:	n/a
2	chr10:97453674-97453724	SK-N-MC	brain:	n/a
3	chr10:97453674-97453724	Hepatocyte	liver:	n/a
4	chr10:97453674-97453724	HCM	heart:	n/a
5	chr10:97453674-97453724	AG04450	lung:	fetal
6	chr10:97453674-97453724	HUVEC	blood vessel:	n/a
7	chr10:97453674-97453724	AG04449	skin:	fetal
8	chr10:97453674-97453724	ProgFib	skin:	n/a
9	chr10:97453674-97453724	PFSK-1	brain:	n/a
10	chr10:97453674-97453724	HepG2	liver:	n/a
11	chr10:97453674-97453724	ovcar-3	ovarian:	n/a
12	chr10:97453674-97453724	NHBE	bronchial:	n/a
13	chr10:97453674-97453724	AG10803	skin:	n/a
14	chr10:97453674-97453724	U87	brain:	n/a
15	chr10:97453674-97453724	GM12891	blood:	n/a
16	chr10:97453674-97453724	A549	lung:	n/a
17	chr10:97453674-97453724	GM19239	blood:	n/a
18	chr10:97453674-97453724	RPTEC	kidney:	n/a
19	chr10:97453674-97453724	LNCaP	prostate:	n/a
20	chr10:97453674-97453724	IMR90	lung:	fetal
21	chr10:97453674-97453724	Jurkat	blood:	n/a
22	chr10:97453674-97453724	Caco-2	colon:	n/a
23	chr10:97453674-97453724	GM12892	blood:	n/a
24	chr10:97453674-97453724	AG09319	gingival:	n/a
25	chr10:97453674-97453724	CMK	blood:	n/a
26	chr10:97453674-97453724	PrEC	prostate:	n/a
27	chr10:97453674-97453724	HRPEpiC	eye:	n/a
28	chr10:97453674-97453724	T-47D	breast:	n/a
29	chr10:97453674-97453724	HCPEpiC	choroid plexus:	n/a
30	chr10:97453674-97453724	MCF-7	breast:	n/a
31	chr10:97453674-97453724	HIPEpiC	eye:	n/a
32	chr10:97453674-97453724	ECC-1	luminal epithelium:	n/a
33	chr10:97453674-97453724	GM06990	blood:	n/a
34	chr10:97453674-97453724	PANC-1	pancreas:	n/a
35	chr10:97453674-97453724	HEK293	kidney:	embryo
36	chr10:97453674-97453724	BE2_C	brain:	n/a
37	chr10:97453674-97453724	HL-60	blood:	n/a
38	chr10:97453674-97453724	HAEpiC	amniotic membrane:	n/a
39	chr10:97453674-97453724	AG09309	skin:	n/a
40	chr10:97453674-97453724	SK-N-SH	brain:	n/a
41	chr10:97453674-97453724	SKMC	muscle:	n/a
42	chr10:97453674-97453724	H1-hESC	embryonic stem cell:	embryo
43	chr10:97453674-97453724	BJ	skin:	n/a
44	chr10:97453674-97453724	HNPCEpiC	eye:	n/a
45	chr10:97453674-97453724	NHDF-neo	bronchial:	n/a
46	chr10:97453674-97453724	HRE	kidney:	n/a
47	chr10:97453674-97453724	HRCEpiC	kidney:	n/a
48	chr10:97453674-97453724	HCT-116	colon:	n/a
49	chr10:97453674-97453724	HPAEpiC	pulmonary alveolar:	n/a
50	chr10:97453674-97453724	NB4	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:97453328..97454140-chr4:2010232..2010748,2	NB4	blood:
2	chr10:97414876..97416556-chr10:97452777..97454283,2	MCF-7	breast:
3	chr10:97416004..97416752-chr10:97453272..97453815,2	MCF-7	breast:
4	chr10:97453319..97454115-chr7:17337855..17338662,2	Hela-S3	cervix:
5	chr10:97453551..97454371-chr10:97667064..97668010,2	MCF-7	breast:

Variant related genes	Relation type
TCTN3	TF binding region
TCTN3	CpG island
ENSG00000106546	Chromatin interaction
ENSG00000226688	Chromatin interaction
ENSG00000173088	Chromatin interaction
ENSG00000185049	Chromatin interaction
ENSG00000059573	Chromatin interaction
ENSG00000237773	Chromatin interaction

Extended variants
information (count: 53 )
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[AFR][1000 genomes];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[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3176892	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3176893	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3181116	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3181118	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3181125	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3181127	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35168849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62625035	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	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7099430	0.87[EUR][1000 genomes]
rs7099515	0.87[EUR][1000 genomes]
rs7101227	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[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7919673	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[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	nsv526180	chr10:97332195-97511037	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41291572	TCTN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97451800-97453800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr10:97452200-97454000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr10:97452200-97454200	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr10:97452400-97453800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr10:97452400-97453800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr10:97452400-97453800	Active TSS	HSMM	muscle
7	chr10:97452400-97454200	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr10:97452400-97454200	Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr10:97452400-97454200	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr10:97452400-97454200	Active TSS	A549	lung
11	chr10:97452400-97454400	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr10:97452600-97453800	Active TSS	H9 Cell Line	embryonic stem cell
13	chr10:97452600-97453800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr10:97452600-97453800	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr10:97452600-97453800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr10:97452600-97453800	Flanking Active TSS	Primary B cells from cord blood	blood
17	chr10:97452600-97453800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
18	chr10:97452600-97453800	Active TSS	NHDF-Ad	bronchial
19	chr10:97452600-97454000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr10:97452600-97454200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr10:97452600-97454200	Active TSS	Ovary	ovary
22	chr10:97452600-97454200	Active TSS	Right Atrium	heart
23	chr10:97452600-97454200	Active TSS	NHLF	lung
24	chr10:97452600-97454400	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr10:97452800-97453800	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr10:97452800-97453800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
27	chr10:97452800-97453800	Active TSS	H1 Cell Line	embryonic stem cell
28	chr10:97452800-97453800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr10:97452800-97453800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr10:97452800-97453800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr10:97452800-97453800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
32	chr10:97452800-97453800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr10:97452800-97453800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
34	chr10:97452800-97453800	Active TSS	Aorta	Aorta
35	chr10:97452800-97453800	Active TSS	Pancreas	Pancrea
36	chr10:97452800-97453800	Active TSS	Stomach Mucosa	stomach
37	chr10:97452800-97453800	Active TSS	HSMMtube	muscle
38	chr10:97452800-97453800	Active TSS	NHEK	skin
39	chr10:97452800-97454000	Active TSS	Fetal Intestine Large	intestine
40	chr10:97452800-97454000	Active TSS	Fetal Muscle Trunk	muscle
41	chr10:97452800-97454000	Active TSS	GM12878-XiMat	blood
42	chr10:97452800-97454200	Active TSS	K562	blood
43	chr10:97453000-97453800	Active TSS	iPS-15b Cell Line	embryonic stem cell
44	chr10:97453000-97453800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr10:97453000-97453800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
46	chr10:97453000-97453800	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr10:97453000-97453800	Active TSS	Gastric	stomach
48	chr10:97453000-97453800	Active TSS	Left Ventricle	heart
49	chr10:97453000-97453800	Active TSS	Lung	lung
50	chr10:97453000-97453800	Active TSS	Psoas Muscle	Psoas

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