Variant report

Variant	rs12078883
Chromosome Location	chr1:228875567-228875568
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:228875351..228875980-chr1:229362943..229363511,2	MCF-7	breast:
2	chr1:228874211..228876992-chr1:228882867..228885336,2	K562	blood:

Variant related genes	Relation type
ENSG00000233920	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10158991	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10916364	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13349	0.94[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];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16848862	0.93[GIH][hapmap]
rs2295256	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35637401	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35832347	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4388674	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4391637	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4500282	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4531263	0.87[CHD][hapmap];0.93[GIH][hapmap]
rs7526487	0.87[CEU][hapmap];0.85[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	nsv1013051	chr1:228786702-228903706	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv997801	chr1:228786702-228975127	Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv870365	chr1:228788356-229267904	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv998255	chr1:228791784-228919202	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv549299	chr1:228793246-229455876	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv468316	chr1:228854703-228919202	Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv549300	chr1:228854703-228919202	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12078883	TMEM63A	cis	cerebellum	SCAN
rs12078883	TRIM17	cis	parietal	SCAN
rs12078883	CNIH4	cis	parietal	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228872400-228876400	Weak transcription	Hela-S3	cervix
2	chr1:228872400-228880200	Weak transcription	Left Ventricle	heart
3	chr1:228872600-228877800	Weak transcription	Primary T cells from cord blood	blood
4	chr1:228872600-228878400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr1:228872600-228880600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:228872600-228881200	Weak transcription	Esophagus	oesophagus
7	chr1:228872600-228884400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr1:228873000-228875800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:228873200-228878400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr1:228873200-228879000	Weak transcription	Ovary	ovary
11	chr1:228873200-228884800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:228873400-228876400	Weak transcription	Fetal Kidney	kidney
13	chr1:228873400-228876400	Enhancers	Stomach Mucosa	stomach
14	chr1:228873400-228879000	Weak transcription	Small Intestine	intestine
15	chr1:228873600-228875600	Transcr. at gene 5' and 3'	Brain Cingulate Gyrus	brain
16	chr1:228873600-228876000	Transcr. at gene 5' and 3'	Brain Substantia Nigra	brain
17	chr1:228873600-228876200	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr1:228873600-228876600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:228873600-228876600	Genic enhancers	Pancreas	Pancrea
20	chr1:228873600-228877000	Genic enhancers	HepG2	liver
21	chr1:228873600-228877200	Genic enhancers	Fetal Thymus	thymus
22	chr1:228873600-228878000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr1:228873600-228878000	Weak transcription	Brain Germinal Matrix	brain
24	chr1:228873600-228878400	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr1:228873600-228878400	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr1:228873600-228879000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr1:228873600-228879000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:228873800-228875800	Genic enhancers	Fetal Muscle Trunk	muscle
29	chr1:228873800-228876600	Genic enhancers	Stomach Smooth Muscle	stomach
30	chr1:228873800-228877200	Genic enhancers	Fetal Intestine Large	intestine
31	chr1:228873800-228878400	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr1:228873800-228878600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr1:228873800-228879000	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr1:228873800-228879000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:228873800-228879000	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr1:228873800-228880200	Weak transcription	Thymus	Thymus
37	chr1:228873800-228882800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:228873800-228884200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr1:228873800-228884200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr1:228874000-228875800	Genic enhancers	Aorta	Aorta
41	chr1:228874000-228876400	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr1:228874000-228876600	Genic enhancers	Primary monocytes fromperipheralblood	blood
43	chr1:228874000-228877200	Genic enhancers	Spleen	Spleen
44	chr1:228874000-228879200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr1:228874000-228879400	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr1:228874000-228881800	Genic enhancers	Liver	Liver
47	chr1:228874200-228875800	Genic enhancers	Monocytes-CD14+_RO01746	blood
48	chr1:228874200-228876600	Genic enhancers	Placenta	Placenta
49	chr1:228874200-228877400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr1:228874200-228878000	Weak transcription	Rectal Smooth Muscle	rectum

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