Variant report

Variant	rs28733606
Chromosome Location	chr12:123845036-123845037
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	POLR2A	chr12:123844771-123845150	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:123844957-123845676	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:123749757..123758492-chr12:123844437..123851411,15	MCF-7	breast:
2	chr12:123844945..123846829-chr12:123847352..123848905,2	MCF-7	breast:
3	chr12:123839316..123842865-chr12:123843251..123845125,3	MCF-7	breast:
4	chr12:123844989..123847500-chr12:124065839..124068689,2	K562	blood:

Variant related genes	Relation type
ENSG00000256092	TF binding region
ENSG00000111328	Chromatin interaction
ENSG00000256092	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10734902	0.93[ASN][1000 genomes]
rs10744152	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10744153	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10744154	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10773012	0.86[ASN][1000 genomes]
rs10773013	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10773018	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10846517	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10846519	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10846520	0.84[ASN][1000 genomes]
rs10846523	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11057283	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11057287	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11612234	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11613711	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28414347	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28417583	0.91[ASN][1000 genomes]
rs28418709	0.93[ASN][1000 genomes]
rs28446728	0.88[ASN][1000 genomes]
rs28501453	0.91[ASN][1000 genomes]
rs28517382	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28537583	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28546238	0.91[ASN][1000 genomes]
rs28587386	0.91[ASN][1000 genomes]
rs28594416	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28595660	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28602967	0.91[ASN][1000 genomes]
rs28605269	0.88[ASN][1000 genomes]
rs28611282	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28613486	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28627651	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28631903	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28681105	0.91[ASN][1000 genomes]
rs28703745	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs28706693	0.86[ASN][1000 genomes]
rs28718696	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs28759130	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28865692	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28885203	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3803001	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3825141	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4759374	0.91[ASN][1000 genomes]
rs4759376	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4759421	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs57356592	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs57416942	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs58537268	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs58948739	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs59295450	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs60755632	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs61058270	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs61751327	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6416289	0.83[ASN][1000 genomes]
rs6488869	0.93[ASN][1000 genomes]
rs6488870	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6488871	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6488872	0.93[ASN][1000 genomes]
rs6488874	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7137243	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7297649	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7297888	0.86[ASN][1000 genomes]
rs7301163	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7310756	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7311304	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7484644	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7485967	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7486223	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7488340	0.93[ASN][1000 genomes]
rs7952835	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7955367	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7959415	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7962723	0.81[ASN][1000 genomes]
rs7970080	0.93[ASN][1000 genomes]
rs7971557	0.88[ASN][1000 genomes]
rs7973131	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7973878	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7977563	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9284166	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9300256	0.93[ASN][1000 genomes]
rs9300257	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9300259	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9669169	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9739008	0.88[ASN][1000 genomes]
rs9739565	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9795593	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv1035223	chr12:123795559-123991706	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv899579	chr12:123843017-123901480	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28733606	KNTC1	cis	frontal cortex	BrainEAC

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123772400-123847800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:123807600-123845200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:123816000-123847400	Weak transcription	Stomach Mucosa	stomach
4	chr12:123820400-123847000	Weak transcription	Fetal Brain Male	brain
5	chr12:123829000-123847400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr12:123830000-123847400	Weak transcription	Brain Substantia Nigra	brain
7	chr12:123830000-123847400	Weak transcription	Colonic Mucosa	Colon
8	chr12:123830000-123847400	Weak transcription	NHLF	lung
9	chr12:123830200-123847400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr12:123830200-123847400	Weak transcription	NHDF-Ad	bronchial
11	chr12:123830200-123847600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr12:123830400-123847600	Weak transcription	Aorta	Aorta
13	chr12:123830600-123847600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr12:123830800-123846600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr12:123830800-123847200	Weak transcription	Hela-S3	cervix
16	chr12:123830800-123847200	Weak transcription	HSMMtube	muscle
17	chr12:123832400-123848200	Weak transcription	Esophagus	oesophagus
18	chr12:123832600-123846400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr12:123832600-123846600	Weak transcription	Spleen	Spleen
20	chr12:123832800-123847000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr12:123832800-123847000	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr12:123832800-123847200	Weak transcription	Brain Anterior Caudate	brain
23	chr12:123832800-123847400	Weak transcription	Osteobl	bone
24	chr12:123832800-123847800	Weak transcription	Fetal Kidney	kidney
25	chr12:123833000-123847000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr12:123833000-123847000	Weak transcription	Stomach Smooth Muscle	stomach
27	chr12:123833800-123847600	Weak transcription	NH-A	brain
28	chr12:123834000-123847000	Weak transcription	Adipose Nuclei	Adipose
29	chr12:123834200-123847000	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr12:123834200-123847400	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr12:123834200-123847400	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr12:123834200-123847400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr12:123834400-123846400	Weak transcription	Brain Hippocampus Middle	brain
34	chr12:123834600-123847400	Weak transcription	NHEK	skin
35	chr12:123834800-123846400	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr12:123834800-123847000	Weak transcription	Placenta	Placenta
37	chr12:123834800-123847600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr12:123835000-123847400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr12:123835000-123847400	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr12:123835000-123847400	Weak transcription	Thymus	Thymus
41	chr12:123835000-123847800	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr12:123835000-123848200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr12:123835200-123847600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr12:123835400-123847400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr12:123835400-123847800	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr12:123835400-123847800	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr12:123836000-123848200	Weak transcription	Gastric	stomach
48	chr12:123837400-123847200	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr12:123837800-123847000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr12:123838800-123847400	Weak transcription	Colon Smooth Muscle	Colon

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