Variant report

Variant	rs10773020
Chromosome Location	chr12:124117089-124117090
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:124116825..124119400-chr12:124154444..124157055,3	MCF-7	breast:
2	chr12:124085449..124088387-chr12:124115552..124120028,6	MCF-7	breast:
3	chr12:123755830..123757417-chr12:124116609..124118455,2	MCF-7	breast:
4	chr12:124068831..124072178-chr12:124116882..124120107,5	K562	blood:
5	chr12:124067567..124070616-chr12:124116717..124118360,3	K562	blood:
6	chr12:124067553..124070106-chr12:124116767..124119854,4	MCF-7	breast:
7	chr12:124116659..124120709-chr12:124455290..124460616,5	K562	blood:
8	chr12:124084988..124092992-chr12:124114351..124121638,14	K562	blood:
9	chr12:124115420..124119615-chr12:124195159..124199573,8	MCF-7	breast:
10	chr12:124085496..124088026-chr12:124116630..124119648,4	MCF-7	breast:
11	chr12:124116424..124121252-chr12:124194298..124198817,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000247373	Chromatin interaction
ENSG00000119242	Chromatin interaction
ENSG00000185344	Chromatin interaction
ENSG00000086598	Chromatin interaction
ENSG00000178882	Chromatin interaction
ENSG00000168778	Chromatin interaction
ENSG00000111364	Chromatin interaction
ENSG00000270095	Chromatin interaction
ENSG00000111328	Chromatin interaction
ENSG00000179195	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10161548	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10773019	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10773021	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10773023	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10773024	0.94[EUR][1000 genomes]
rs10773025	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10846530	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10846532	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10846534	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10846536	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10846538	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10846539	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10846542	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10846543	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10846545	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11057299	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11057304	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11057310	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057312	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11057313	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11057322	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11057329	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11057331	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11057332	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11057336	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11572926	0.92[ASN][1000 genomes]
rs11572940	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11572949	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12231444	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12308953	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12309685	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12313119	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17840832	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2292702	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2707	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3704	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3748270	0.95[ASN][1000 genomes]
rs3748271	0.94[EUR][1000 genomes]
rs3850952	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs3923720	0.95[ASN][1000 genomes]
rs4930713	0.88[CHD][hapmap]
rs4930714	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs61154946	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6488887	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7298287	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7302177	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7303409	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7307219	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7311689	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7316410	0.95[ASN][1000 genomes]
rs73414223	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7358562	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7967780	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9919	0.86[CHB][hapmap];0.94[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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
6	esv2757517	chr12:124110122-124195856	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
7	esv2759918	chr12:124110122-124195856	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS 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	22 gene(s)	inside rSNPs	diseases
8	nsv1041918	chr12:124115035-124184855	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
9	nsv1042866	chr12:124115035-124195856	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv442292	chr12:124115047-124195854	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10773020	TCTN2	cis	lung	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124095000-124117600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:124096400-124117600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:124102400-124117600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr12:124112200-124117400	Weak transcription	Psoas Muscle	Psoas
5	chr12:124113600-124117600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:124113800-124117400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr12:124113800-124117400	Weak transcription	Small Intestine	intestine
8	chr12:124114000-124117800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:124114800-124117600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr12:124115000-124117400	Weak transcription	HUVEC	blood vessel
11	chr12:124115000-124117600	Weak transcription	Stomach Mucosa	stomach
12	chr12:124115400-124117400	Weak transcription	Right Ventricle	heart
13	chr12:124115400-124117600	Weak transcription	Esophagus	oesophagus
14	chr12:124115800-124117200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr12:124115800-124117400	Weak transcription	HSMM	muscle
16	chr12:124116000-124117200	Weak transcription	HepG2	liver
17	chr12:124116000-124117200	Weak transcription	Osteobl	bone
18	chr12:124116000-124117400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr12:124116000-124117400	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr12:124116000-124117400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr12:124116000-124117400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr12:124116000-124117400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr12:124116000-124117400	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr12:124116000-124117400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr12:124116000-124117400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr12:124116000-124117400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr12:124116000-124117400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr12:124116000-124117400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr12:124116000-124117400	Weak transcription	Primary T cells from cord blood	blood
30	chr12:124116000-124117400	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr12:124116000-124117400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr12:124116000-124117400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr12:124116000-124117400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr12:124116000-124117400	Weak transcription	Adipose Nuclei	Adipose
35	chr12:124116000-124117400	Weak transcription	Brain Cingulate Gyrus	brain
36	chr12:124116000-124117400	Weak transcription	Fetal Intestine Large	intestine
37	chr12:124116000-124117400	Weak transcription	Fetal Kidney	kidney
38	chr12:124116000-124117400	Weak transcription	Fetal Lung	lung
39	chr12:124116000-124117400	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr12:124116000-124117400	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr12:124116000-124117400	Weak transcription	NH-A	brain
42	chr12:124116000-124117400	Weak transcription	NHLF	lung
43	chr12:124116000-124117600	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr12:124116000-124117600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr12:124116000-124117600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr12:124116000-124117600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr12:124116000-124117600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr12:124116000-124117600	Weak transcription	Brain Angular Gyrus	brain
49	chr12:124116000-124117600	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr12:124116000-124117600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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