Variant report

Variant	rs786444
Chromosome Location	chr12:124065416-124065417
allele	C/T
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	FOS	chr12:124065414-124065712	HUVEC	blood vessel:	n/a	chr12:124065556-124065567

No.	Distal block	Cell Line	Cell type
1	chr12:124057277..124059073-chr12:124064975..124067218,3	MCF-7	breast:
2	chr12:123870366..123875219-chr12:124064500..124069174,6	K562	blood:
3	chr12:123872778..123876196-chr12:124065295..124071344,6	MCF-7	breast:

Variant related genes	Relation type
TMED2	TF binding region
ENSG00000183955	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs1051793	0.80[CEU][hapmap]
rs1060637	0.88[CEU][hapmap]
rs10846531	0.89[CHB][hapmap];0.91[CHD][hapmap];0.84[ASN][1000 genomes]
rs10846535	0.89[CEU][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10846537	0.85[CEU][hapmap]
rs11057307	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057320	0.80[EUR][1000 genomes]
rs11572920	0.88[CEU][hapmap]
rs11572952	0.81[CEU][hapmap]
rs11609591	0.89[CEU][hapmap]
rs11611354	0.85[CEU][hapmap]
rs11612030	0.88[CEU][hapmap]
rs11612479	0.85[CEU][hapmap]
rs11612927	0.84[CEU][hapmap]
rs11613632	0.84[CEU][hapmap]
rs11615300	0.81[EUR][1000 genomes]
rs12817757	0.84[CEU][hapmap]
rs12820195	0.85[CEU][hapmap]
rs12821242	0.87[CEU][hapmap]
rs12827074	0.85[CEU][hapmap]
rs12829893	0.88[CEU][hapmap]
rs12830927	0.88[CEU][hapmap]
rs1515814	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1515815	0.88[CEU][hapmap]
rs2048802	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs2222060	0.81[CEU][hapmap]
rs2250026	0.85[CEU][hapmap]
rs3748268	0.89[CHB][hapmap];0.91[CHD][hapmap];0.84[ASN][1000 genomes]
rs3748269	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4040225	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4456350	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4930708	0.85[CEU][hapmap];0.84[MEX][hapmap]
rs6488883	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488888	0.81[CEU][hapmap]
rs6488893	0.85[CEU][hapmap]
rs6488897	0.89[CEU][hapmap];0.84[MEX][hapmap]
rs6551	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7133199	0.88[CEU][hapmap]
rs7134074	0.88[CEU][hapmap]
rs7134896	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7135660	0.84[CEU][hapmap]
rs7136939	0.85[CEU][hapmap]
rs7137946	0.92[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs7139193	0.92[CEU][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs7294984	0.81[CEU][hapmap]
rs7297576	0.89[CEU][hapmap];0.84[MEX][hapmap]
rs7298440	0.85[CEU][hapmap]
rs7298831	0.88[CEU][hapmap]
rs7302183	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7302649	0.85[CEU][hapmap]
rs7306549	0.89[CEU][hapmap];0.84[MEX][hapmap]
rs7307008	0.88[CEU][hapmap]
rs7307343	0.85[CEU][hapmap]
rs7308234	0.82[CEU][hapmap]
rs7308862	0.89[CEU][hapmap];0.84[MEX][hapmap]
rs7309528	0.85[CEU][hapmap]
rs7310918	0.85[CEU][hapmap]
rs7313032	0.89[CEU][hapmap];0.84[MEX][hapmap]
rs7313261	0.89[CEU][hapmap]
rs7313628	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7399224	0.85[CEU][hapmap]
rs786422	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786423	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786425	0.88[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786441	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs786443	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786445	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786447	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786448	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786449	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786452	0.86[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs786454	0.91[AFR][1000 genomes]
rs7953599	0.85[CEU][hapmap]
rs7958693	0.92[CEU][hapmap];0.84[MEX][hapmap]
rs7959553	0.84[CEU][hapmap]
rs7963968	0.85[CEU][hapmap]
rs7964443	0.89[CEU][hapmap];0.84[MEX][hapmap]
rs7966867	0.92[CEU][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap]
rs7966882	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7972413	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7973155	0.84[CEU][hapmap]
rs7973695	0.84[CEU][hapmap]
rs7974279	0.89[CEU][hapmap]
rs7975119	0.85[CEU][hapmap]
rs7975233	0.85[CEU][hapmap]
rs7978447	0.85[CEU][hapmap]
rs7979528	0.85[CEU][hapmap]
rs884892	0.89[CHB][hapmap];0.91[CHD][hapmap];0.84[ASN][1000 genomes]
rs908373	0.92[CEU][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9919	0.83[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	esv2422416	chr12:124009676-124085689	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs786444	TCTN2	cis	cerebellum	SCAN
rs786444	SETD1B	cis	parietal	SCAN
rs786444	ABCB9	cis	parietal	SCAN
rs786444	TCTN2	cis	Artery Tibial	GTEx
rs786444	TCTN2	cis	parietal	SCAN
rs786444	TCTN2	cis	Adipose Subcutaneous	GTEx
rs786444	DDX55	cis	parietal	SCAN
rs786444	CABP1	cis	cerebellum	SCAN
rs786444	DDX55	cis	cerebellum	SCAN
rs786444	DDX55	cis	multi-tissue	Pritchard

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124055000-124067400	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr12:124055200-124068000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:124055400-124067800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:124056000-124066600	Weak transcription	Fetal Muscle Leg	muscle
5	chr12:124056000-124066600	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr12:124056000-124067000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr12:124056000-124067800	Weak transcription	Lung	lung
8	chr12:124056200-124066600	Weak transcription	Thymus	Thymus
9	chr12:124056200-124067000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr12:124056200-124067200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr12:124056400-124066600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr12:124056400-124066600	Weak transcription	Adipose Nuclei	Adipose
13	chr12:124056400-124066600	Weak transcription	Brain Anterior Caudate	brain
14	chr12:124056400-124066600	Weak transcription	K562	blood
15	chr12:124056400-124066800	Weak transcription	Brain Hippocampus Middle	brain
16	chr12:124056400-124066800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr12:124056400-124067000	Weak transcription	NHDF-Ad	bronchial
18	chr12:124056400-124067400	Weak transcription	HSMMtube	muscle
19	chr12:124056800-124066600	Weak transcription	Dnd41	blood
20	chr12:124058800-124066600	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr12:124058800-124067000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr12:124059200-124066800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr12:124059200-124066800	Weak transcription	Spleen	Spleen
24	chr12:124059200-124067200	Weak transcription	Brain Germinal Matrix	brain
25	chr12:124059400-124066600	Weak transcription	Liver	Liver
26	chr12:124059400-124067000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr12:124059400-124067200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr12:124059800-124066600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr12:124059800-124066800	Weak transcription	Fetal Kidney	kidney
30	chr12:124060000-124066800	Weak transcription	Ovary	ovary
31	chr12:124060000-124067000	Weak transcription	NHLF	lung
32	chr12:124060400-124066000	Weak transcription	Primary B cells from cord blood	blood
33	chr12:124060400-124066600	Weak transcription	HSMM	muscle
34	chr12:124060400-124066800	Weak transcription	Gastric	stomach
35	chr12:124060600-124066800	Weak transcription	GM12878-XiMat	blood
36	chr12:124061000-124066000	Weak transcription	Fetal Muscle Trunk	muscle
37	chr12:124061000-124066600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr12:124061000-124066800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr12:124061000-124066800	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr12:124061000-124067000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr12:124061200-124066800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr12:124061200-124067000	Weak transcription	Fetal Lung	lung
43	chr12:124061200-124067200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr12:124061400-124066600	Weak transcription	Fetal Thymus	thymus
45	chr12:124061400-124066800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr12:124061400-124066800	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr12:124061400-124067000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr12:124061600-124066600	Weak transcription	Primary hematopoietic stem cells	blood
49	chr12:124061600-124067000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr12:124061800-124066800	Weak transcription	Brain Angular Gyrus	brain

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