Variant report

Variant	rs12030478
Chromosome Location	chr1:211755204-211755205
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	E2F4	chr1:211754940-211755210	MCF10A-Er-Src	breast:	n/a	n/a
2	TBL1XR1	chr1:211755086-211755782	GM12878	blood:	n/a	n/a
3	FOS	chr1:211754842-211755301	MCF10A-Er-Src	breast:	n/a	chr1:211755065-211755074
4	PBX3	chr1:211754805-211755283	SK-N-SH	brain:	n/a	n/a
5	MEF2A	chr1:211754777-211755477	SK-N-SH	brain:	n/a	n/a
6	CUX1	chr1:211755194-211755679	GM12878	blood:	n/a	n/a
7	MEF2A	chr1:211754760-211755501	SK-N-SH	brain:	n/a	n/a
8	CEBPB	chr1:211754791-211755264	IMR90	lung:	n/a	chr1:211754812-211754824

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:211752607..211756285-chr1:211771490..211773503,3	K562	blood:

Variant related genes	Relation type
SLC30A1	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12026206	0.89[JPT][hapmap]
rs12030590	0.87[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs726986	0.89[CEU][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes]
rs989636	0.85[EUR][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	nsv832514	chr1:211630247-211794963	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	esv1796467	chr1:211726975-211769893	Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	esv1840920	chr1:211726975-211769893	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	esv1791933	chr1:211751208-211755204	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
5	esv1793880	chr1:211751208-211755204	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12030478	C1orf227	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:211753200-211755600	Enhancers	Small Intestine	intestine
2	chr1:211753200-211757000	Weak transcription	Spleen	Spleen
3	chr1:211753400-211755400	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr1:211753400-211755600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:211753400-211755800	Enhancers	NH-A	brain
6	chr1:211753400-211756800	Weak transcription	Aorta	Aorta
7	chr1:211753400-211757000	Enhancers	Primary hematopoietic stem cells	blood
8	chr1:211753400-211757000	Enhancers	Adipose Nuclei	Adipose
9	chr1:211753400-211757000	Weak transcription	Right Atrium	heart
10	chr1:211753400-211757600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:211753600-211755400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:211753600-211755600	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr1:211753600-211755600	Enhancers	NHLF	lung
14	chr1:211753600-211756000	Enhancers	Colon Smooth Muscle	Colon
15	chr1:211753600-211756400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr1:211753600-211756800	Enhancers	Osteobl	bone
17	chr1:211753600-211757200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr1:211753800-211755400	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr1:211753800-211755600	Weak transcription	Fetal Muscle Leg	muscle
20	chr1:211753800-211755600	Enhancers	Rectal Smooth Muscle	rectum
21	chr1:211753800-211755600	Weak transcription	Stomach Smooth Muscle	stomach
22	chr1:211753800-211756800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:211753800-211757200	Enhancers	Fetal Intestine Large	intestine
24	chr1:211753800-211757400	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr1:211753800-211757400	Enhancers	Fetal Intestine Small	intestine
26	chr1:211753800-211758000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:211754000-211755400	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr1:211754000-211756600	Weak transcription	Placenta	Placenta
29	chr1:211754000-211756800	Enhancers	HepG2	liver
30	chr1:211754000-211765400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:211754200-211755600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:211754600-211755400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr1:211754600-211756000	Weak transcription	Duodenum Mucosa	Duodenum
34	chr1:211754600-211756200	Enhancers	Rectal Mucosa Donor 29	rectum
35	chr1:211754800-211755400	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr1:211754800-211755400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr1:211754800-211755600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr1:211754800-211755600	Enhancers	Muscle Satellite Cultured Cells	--
39	chr1:211754800-211755800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:211754800-211756600	Enhancers	NHDF-Ad	bronchial
41	chr1:211754800-211756800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr1:211755000-211755600	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr1:211755000-211755600	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr1:211755000-211755600	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr1:211755000-211755600	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr1:211755000-211755600	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr1:211755000-211755600	Enhancers	HSMMtube	muscle
48	chr1:211755000-211756000	Enhancers	Primary T cells fromperipheralblood	blood
49	chr1:211755000-211756200	Enhancers	Primary B cells from peripheral blood	blood
50	chr1:211755000-211756400	Weak transcription	K562	blood

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