Variant report

Variant	rs6488883
Chromosome Location	chr12:124101347-124101348
allele	C/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	POLR2A	chr12:124101185-124101641	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr12:124101244-124102379	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:124101332-124101547	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr12:124101033-124101385	K562	blood:	n/a	n/a
5	POLR2A	chr12:124100893-124101786	K562	blood:	n/a	n/a
6	POLR2A	chr12:124100783-124102504	K562	blood:	n/a	n/a
7	POLR2A	chr12:124101027-124101366	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:124086555..124088221-chr12:124100026..124101762,2	K562	blood:
2	chr12:124088481..124090749-chr12:124100690..124102961,3	K562	blood:

Variant related genes	Relation type
DDX55	TF binding region
ENSG00000111364	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10846531	0.84[ASN][1000 genomes]
rs10846535	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11057307	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057320	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11615300	0.86[EUR][1000 genomes]
rs12813346	0.80[EUR][1000 genomes]
rs12821219	0.81[EUR][1000 genomes]
rs1515814	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2048802	0.84[ASN][1000 genomes]
rs2222061	0.81[EUR][1000 genomes]
rs3748268	0.84[ASN][1000 genomes]
rs3748269	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4040225	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4456350	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6551	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7134896	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7135624	0.84[EUR][1000 genomes]
rs7137946	0.82[EUR][1000 genomes]
rs7139193	0.82[EUR][1000 genomes]
rs7301907	0.82[EUR][1000 genomes]
rs7302183	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7302449	0.82[EUR][1000 genomes]
rs7313628	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs786422	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786423	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786425	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786441	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs786443	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786444	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786445	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786447	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786448	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786449	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786452	0.90[ASN][1000 genomes]
rs7966867	0.81[EUR][1000 genomes]
rs7966882	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7971452	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7972413	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs884892	0.84[ASN][1000 genomes]
rs908373	0.86[EUR][1000 genomes];0.81[ASN][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	nsv1050598	chr12:123991646-124214332	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv541623	chr12:123991646-124214332	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
4	nsv1042181	chr12:124037400-124152950	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1040356	chr12:124094758-124172731	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6488883	TCTN2	cis	Adipose Subcutaneous	GTEx
rs6488883	TCTN2	cis	Artery Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124087800-124102000	Weak transcription	Stomach Mucosa	stomach
2	chr12:124087800-124109600	Weak transcription	Right Atrium	heart
3	chr12:124088000-124107200	Strong transcription	K562	blood
4	chr12:124088200-124116000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:124088200-124117000	Strong transcription	Fetal Stomach	stomach
6	chr12:124088400-124102400	Strong transcription	HUVEC	blood vessel
7	chr12:124088400-124103000	Strong transcription	Left Ventricle	heart
8	chr12:124088400-124105800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr12:124088400-124108000	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr12:124088400-124116000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr12:124088400-124116000	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr12:124088400-124116000	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr12:124088400-124116000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr12:124088400-124116000	Strong transcription	Sigmoid Colon	Sigmoid Colon
15	chr12:124088400-124116200	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr12:124088400-124116800	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr12:124088400-124117000	Strong transcription	Fetal Intestine Small	intestine
18	chr12:124088600-124103000	Strong transcription	Lung	lung
19	chr12:124088600-124104800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr12:124088600-124107400	Strong transcription	H9 Cell Line	embryonic stem cell
21	chr12:124088600-124116000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr12:124088600-124116000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr12:124088600-124116000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr12:124088600-124116000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr12:124088600-124116000	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr12:124088600-124116000	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr12:124088600-124116200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr12:124088600-124116200	Strong transcription	Fetal Thymus	thymus
29	chr12:124088600-124116800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr12:124088600-124116800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr12:124088600-124116800	Strong transcription	Fetal Muscle Trunk	muscle
32	chr12:124088600-124117000	Strong transcription	Primary B cells from peripheral blood	blood
33	chr12:124088800-124102800	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr12:124088800-124107600	Strong transcription	NH-A	brain
35	chr12:124088800-124116000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:124088800-124116000	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr12:124088800-124116000	Strong transcription	Fetal Intestine Large	intestine
38	chr12:124089000-124105800	Strong transcription	Fetal Muscle Leg	muscle
39	chr12:124089000-124107400	Strong transcription	Fetal Lung	lung
40	chr12:124089000-124116000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr12:124089000-124116200	Strong transcription	Brain Germinal Matrix	brain
42	chr12:124089200-124107400	Strong transcription	Hela-S3	cervix
43	chr12:124089200-124115400	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr12:124089200-124116000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr12:124089200-124116000	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr12:124089200-124116000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr12:124089200-124116200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr12:124089200-124116400	Strong transcription	Liver	Liver
49	chr12:124089200-124116600	Strong transcription	Stomach Smooth Muscle	stomach
50	chr12:124089600-124101800	Strong transcription	Brain Hippocampus Middle	brain

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