Variant report

Variant	rs12041975
Chromosome Location	chr1:94336935-94336936
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:94333938-94341380	K562	blood:	n/a	n/a
2	POLR2A	chr1:94336792-94337706	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:94312529..94314745-chr1:94335727..94337365,2	MCF-7	breast:
2	chr1:94336837..94340766-chr1:94341847..94346212,6	K562	blood:
3	chr1:94335249..94337846-chr1:94338670..94340764,2	K562	blood:
4	chr1:94310035..94314107-chr1:94336308..94338315,4	K562	blood:
5	chr1:94311309..94313221-chr1:94336029..94338174,3	K562	blood:
6	chr1:94336863..94338499-chr1:94348884..94351600,2	K562	blood:

No data

Variant related genes	Relation type
DNTTIP2	TF binding region
ENSG00000137936	Chromatin interaction
ENSG00000260464	Chromatin interaction
ENSG00000211575	Chromatin interaction
ENSG00000067334	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10489602	0.83[JPT][hapmap]
rs10489604	0.89[CHB][hapmap];0.87[JPT][hapmap]
rs1051394	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11165021	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11165022	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11165023	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11165025	0.87[ASN][1000 genomes]
rs11165026	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12029548	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12029637	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12029670	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12140446	0.83[JPT][hapmap]
rs12758972	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1884018	0.89[CHB][hapmap];0.87[JPT][hapmap]
rs2092698	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2092699	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2103784	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2143992	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2235971	0.89[CHB][hapmap];0.87[JPT][hapmap]
rs2273165	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2273166	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.82[LWK][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2391315	0.85[CEU][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap]
rs2391321	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2391322	0.89[CHB][hapmap];0.87[JPT][hapmap]
rs2747045	0.83[JPT][hapmap]
rs3747965	0.89[CHB][hapmap];0.87[JPT][hapmap]
rs3789459	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3789460	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4075523	0.83[JPT][hapmap]
rs4141737	0.89[CHB][hapmap];0.87[JPT][hapmap]
rs4240956	0.83[JPT][hapmap]
rs4847191	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4847193	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4847263	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4847264	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6663218	0.84[CHB][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap]
rs6664719	0.89[CHB][hapmap];0.87[JPT][hapmap]
rs6664876	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6666633	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6667991	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6681169	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6681265	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6684054	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6697189	0.87[ASN][1000 genomes]
rs7364663	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs743111	0.84[CHB][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap]
rs7513489	0.87[ASN][1000 genomes]
rs7513786	0.90[ASN][1000 genomes]
rs7514828	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7517632	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7518940	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7555136	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7556047	0.83[ASN][1000 genomes]
rs7556107	0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998755	chr1:94294015-94341712	Flanking Active TSS Active TSS Genic enhancers Enhancers Weak transcription Strong transcription 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	121 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12041975	RP11-488P3.1	cis	Thyroid	GTEx
rs12041975	RP11-488P3.1	cis	Skin Sun Exposed Lower leg	GTEx
rs12041975	RP11-488P3.1	cis	lung	GTEx
rs12041975	RP11-488P3.1	cis	Muscle Skeletal	GTEx
rs12041975	RP11-488P3.1	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94322200-94343600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:94329800-94343600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:94330000-94337000	Weak transcription	Psoas Muscle	Psoas
4	chr1:94330000-94338800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:94330600-94343600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:94331000-94339000	Weak transcription	Pancreas	Pancrea
7	chr1:94332400-94342000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:94332800-94337000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:94332800-94337000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:94332800-94339600	Weak transcription	Stomach Mucosa	stomach
11	chr1:94332800-94340800	Strong transcription	Left Ventricle	heart
12	chr1:94332800-94341400	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr1:94332800-94341600	Strong transcription	Primary B cells from peripheral blood	blood
14	chr1:94332800-94341600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:94332800-94341800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr1:94332800-94341800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:94332800-94341800	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr1:94332800-94343200	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr1:94332800-94343200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:94333000-94337000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:94333000-94341600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:94333000-94342000	Strong transcription	Fetal Brain Female	brain
23	chr1:94333200-94341600	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr1:94333200-94341600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:94333200-94343200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr1:94333400-94341600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:94333600-94341800	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr1:94333800-94341200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:94333800-94341600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr1:94333800-94343000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:94334000-94340800	Strong transcription	Brain Anterior Caudate	brain
32	chr1:94334000-94341200	Strong transcription	Primary T cells from cord blood	blood
33	chr1:94334000-94341200	Strong transcription	Primary hematopoietic stem cells	blood
34	chr1:94334000-94341600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:94334000-94341600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr1:94334000-94341600	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr1:94334000-94341800	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr1:94334000-94341800	Strong transcription	Fetal Kidney	kidney
39	chr1:94334000-94341800	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr1:94334000-94342000	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr1:94334000-94343000	Strong transcription	Fetal Thymus	thymus
42	chr1:94334000-94343400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr1:94334200-94337600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
44	chr1:94334200-94337600	Strong transcription	Brain Angular Gyrus	brain
45	chr1:94334200-94339200	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr1:94334200-94339400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr1:94334200-94340800	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr1:94334200-94341200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
49	chr1:94334200-94341600	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr1:94334200-94341600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood

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