Variant report

Variant	rs3176892
Chromosome Location	chr10:97515588-97515589
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	PML	chr10:97515345-97516523	GM12878	blood:	n/a	n/a
2	NFATC1	chr10:97515053-97517578	GM12878	blood:	n/a	n/a
3	POLR2A	chr10:97515141-97519960	GM12878	blood:	n/a	n/a
4	POLR2A	chr10:97515142-97517519	GM12891	blood:	n/a	n/a
5	TAF1	chr10:97515281-97516032	GM12891	blood:	n/a	n/a
6	RUNX3	chr10:97515028-97516089	GM12878	blood:	n/a	n/a
7	SP1	chr10:97515100-97515648	GM12878	blood:	n/a	n/a
8	FOXM1	chr10:97515160-97515951	GM12878	blood:	n/a	n/a
9	POLR2A	chr10:97515231-97519894	GM12892	blood:	n/a	n/a
10	POLR2A	chr10:97514833-97520109	GM12891	blood:	n/a	n/a
11	CREB1	chr10:97515083-97515721	GM12878	blood:	n/a	n/a
12	ELF1	chr10:97515110-97515646	GM12878	blood:	n/a	n/a
13	POLR2A	chr10:97514706-97520659	GM12878	blood:	n/a	n/a
14	TBL1XR1	chr10:97514908-97519757	GM12878	blood:	n/a	n/a
15	RELA	chr10:97515332-97516865	GM15510	blood:	n/a	n/a
16	POLR2A	chr10:97515142-97520214	GM12892	blood:	n/a	n/a
17	RFX5	chr10:97515022-97515592	HepG2	liver:	n/a	n/a
18	SETDB1	chr10:97515004-97515702	U2OS	brain:	n/a	n/a
19	KAP1	chr10:97515124-97515626	HEK293	kidney:	n/a	n/a
20	POLR2A	chr10:97515056-97520623	GM12878	blood:	n/a	n/a
21	RFX5	chr10:97515192-97515601	K562	blood:	n/a	n/a
22	MXI1	chr10:97515356-97517411	GM12878	blood:	n/a	n/a
23	POLR2A	chr10:97514895-97520560	GM12878	blood:	n/a	n/a
24	STAT3	chr10:97515541-97515715	MCF10A-Er-Src	breast:	n/a	n/a
25	RELA	chr10:97515082-97517421	GM19099	blood:	n/a	n/a
26	CUX1	chr10:97515135-97516867	GM12878	blood:	n/a	n/a
27	BCLAF1	chr10:97515160-97517556	GM12878	blood:	n/a	n/a
28	CREB1	chr10:97514964-97517574	GM12878	blood:	n/a	n/a
29	IKZF1	chr10:97515182-97516241	GM12878	blood:	n/a	n/a
30	ZNF143	chr10:97515228-97515858	GM12878	blood:	n/a	n/a
31	SMC3	chr10:97515273-97516561	GM12878	blood:	n/a	n/a
32	NFATC1	chr10:97515138-97517557	GM12878	blood:	n/a	n/a
33	POLR2A	chr10:97515083-97519247	GM18526	blood:	n/a	n/a
34	BCLAF1	chr10:97515135-97518951	GM12878	blood:	n/a	chr10:97518560-97518569 chr10:97517901-97517910
35	STAT5A	chr10:97515043-97517568	GM12878	blood:	n/a	chr10:97516797-97516805 chr10:97516619-97516627
36	TBP	chr10:97515294-97515610	H1-hESC	embryonic stem cell:	n/a	n/a
37	CHD1	chr10:97515562-97516290	H1-hESC	embryonic stem cell:	n/a	n/a
38	NFIC	chr10:97514909-97516636	GM12878	blood:	n/a	n/a
39	STAT5A	chr10:97515305-97516901	GM12878	blood:	n/a	chr10:97516797-97516805 chr10:97516619-97516627
40	POLR2A	chr10:97515084-97519972	GM12892	blood:	n/a	n/a
41	ATF2	chr10:97515215-97518863	GM12878	blood:	n/a	n/a
42	TAF1	chr10:97515282-97515672	GM12878	blood:	n/a	n/a
43	TAF1	chr10:97515317-97515624	GM12892	blood:	n/a	n/a
44	USF2	chr10:97515215-97515631	GM12878	blood:	n/a	n/a
45	RELA	chr10:97515295-97517477	GM12878	blood:	n/a	n/a
46	POLR2A	chr10:97514910-97520584	GM12891	blood:	n/a	n/a
47	POU2F2	chr10:97515115-97519316	GM12878	blood:	n/a	chr10:97518600-97518613
48	TBP	chr10:97515032-97519087	GM12878	blood:	n/a	n/a
49	CHD1	chr10:97515071-97519699	GM12878	blood:	n/a	n/a
50	POLR2A	chr10:97515148-97520513	GM18505	blood:	n/a	n/a

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

Variant related genes	Relation type
ENTPD1	TF binding region

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10882622	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs10882623	0.87[EUR][1000 genomes]
rs10882624	0.87[EUR][1000 genomes]
rs10882626	1.00[CEU][hapmap];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	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs11188369	1.00[CEU][hapmap];1.00[MEX][hapmap];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[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12218873	0.87[EUR][1000 genomes]
rs12242866	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs12242918	1.00[CEU][hapmap];1.00[MEX][hapmap];0.87[EUR][1000 genomes]
rs12242923	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs12248661	1.00[CEU][hapmap];1.00[MEX][hapmap];0.87[EUR][1000 genomes]
rs12250514	1.00[CEU][hapmap];1.00[MEX][hapmap];0.87[EUR][1000 genomes]
rs12255572	1.00[CEU][hapmap];1.00[MEX][hapmap];0.87[EUR][1000 genomes]
rs3176887	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3176893	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3181116	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3181118	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3181125	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3181127	1.00[CEU][hapmap];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]
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[CEU][hapmap];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	1.00[CEU][hapmap];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[CEU][hapmap];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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3176892	TCTN3	Cis_1M	lymphoblastoid	RTeQTL
rs3176892	TCTN3	cis	lymphoblastoid	seeQTL

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97514600-97515600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr10:97514600-97516800	Active TSS	Primary hematopoietic stem cells	blood
3	chr10:97514800-97515600	Enhancers	Primary B cells from peripheral blood	blood
4	chr10:97515000-97515600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr10:97515000-97515600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr10:97515000-97516200	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr10:97515000-97516600	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr10:97515000-97518200	Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr10:97515000-97518400	Active TSS	Stomach Smooth Muscle	stomach
10	chr10:97515200-97515600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
11	chr10:97515200-97515600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr10:97515200-97515600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
13	chr10:97515200-97515800	Enhancers	Placenta	Placenta
14	chr10:97515200-97516000	Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr10:97515200-97516000	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr10:97515200-97516200	Flanking Active TSS	Primary B cells from cord blood	blood
17	chr10:97515200-97516200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
18	chr10:97515200-97516400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr10:97515200-97516600	Active TSS	H9 Cell Line	embryonic stem cell
20	chr10:97515200-97516600	Active TSS	Psoas Muscle	Psoas
21	chr10:97515200-97516600	Weak transcription	Small Intestine	intestine
22	chr10:97515200-97516800	Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr10:97515200-97516800	Active TSS	Brain Cingulate Gyrus	brain
24	chr10:97515200-97517000	Active TSS	Fetal Intestine Small	intestine
25	chr10:97515200-97517400	Active TSS	Brain Anterior Caudate	brain
26	chr10:97515200-97517400	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr10:97515200-97517600	Active TSS	Colonic Mucosa	Colon
28	chr10:97515200-97518200	Active TSS	Duodenum Mucosa	Duodenum
29	chr10:97515200-97518200	Active TSS	GM12878-XiMat	blood
30	chr10:97515200-97518400	Active TSS	Brain Hippocampus Middle	brain
31	chr10:97515200-97518600	Active TSS	Rectal Mucosa Donor 29	rectum
32	chr10:97515400-97515600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr10:97515400-97515600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr10:97515400-97515600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr10:97515400-97515600	Bivalent/Poised TSS	Left Ventricle	heart
36	chr10:97515400-97515600	Enhancers	NHDF-Ad	bronchial
37	chr10:97515400-97515800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
38	chr10:97515400-97515800	Enhancers	K562	blood
39	chr10:97515400-97516200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr10:97515400-97516200	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
41	chr10:97515400-97516200	Bivalent/Poised TSS	A549	lung
42	chr10:97515400-97516400	Active TSS	HUES64 Cell Line	embryonic stem cell
43	chr10:97515400-97516400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
44	chr10:97515400-97516400	Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr10:97515400-97516600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
46	chr10:97515400-97516600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr10:97515400-97516600	Active TSS	Fetal Stomach	stomach
48	chr10:97515400-97516600	Active TSS	Ovary	ovary
49	chr10:97515400-97516600	Active TSS	Right Ventricle	heart
50	chr10:97515400-97516800	Active TSS	H1 Cell Line	embryonic stem cell

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