Variant report

Variant	rs2936025
Chromosome Location	chr1:222836894-222836895
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:222829766-222841488	K562	blood:	n/a	n/a
2	POLR2A	chr1:222836872-222837274	U87	brain:	n/a	n/a
3	POLR2A	chr1:222836744-222837997	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:222832045..222836526-chr1:222836686..222840322,4	K562	blood:
2	chr1:222817247..222819039-chr1:222835684..222838634,2	MCF-7	breast:
3	chr1:222836221..222837854-chr1:222884380..222886530,2	MCF-7	breast:
4	chr1:222831415..222835034-chr1:222836686..222839635,4	K562	blood:
5	chr1:222816933..222819100-chr1:222834674..222837406,2	K562	blood:
6	chr1:222836136..222838189-chr1:222847780..222849818,2	MCF-7	breast:

No data

Variant related genes	Relation type
MIA3	TF binding region
ENSG00000272750	TF binding region
ENSG00000154305	Chromatin interaction
ENSG00000162819	Chromatin interaction
ENSG00000272750	Chromatin interaction
ENSG00000186063	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1053316	0.89[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs1986348	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2291833	0.91[ASN][1000 genomes]
rs2936019	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2936024	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2936026	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2936056	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2936057	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3002137	0.83[EUR][1000 genomes]
rs3002138	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3002140	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3002150	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3008599	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3008600	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3008603	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3008605	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3008611	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3008613	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3008620	0.85[ASN][1000 genomes]
rs3008624	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3008627	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3008628	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3008632	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3008633	0.95[CHD][hapmap];0.85[JPT][hapmap]
rs3008634	0.95[CHD][hapmap];0.85[JPT][hapmap]
rs3008635	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3008639	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34290674	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34851033	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35684750	0.81[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap]
rs35762933	0.81[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap]
rs4379681	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs73124815	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73124822	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73124862	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs73124880	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73124889	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73124891	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73126803	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73126812	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73126814	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[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	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873205	chr1:222718718-222923351	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2936025	BROX	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222818800-222841600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:222819000-222841800	Strong transcription	HUES64 Cell Line	embryonic stem cell
3	chr1:222819200-222841400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:222819200-222841600	Strong transcription	Placenta	Placenta
5	chr1:222819400-222841200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr1:222820000-222838800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:222820000-222841400	Strong transcription	HSMM	muscle
8	chr1:222820000-222841600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:222820200-222838800	Strong transcription	NHDF-Ad	bronchial
10	chr1:222820200-222841400	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr1:222820200-222841400	Strong transcription	NH-A	brain
12	chr1:222820400-222841800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr1:222820600-222841200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:222820600-222841400	Strong transcription	Rectal Mucosa Donor 31	rectum
15	chr1:222820800-222841000	Strong transcription	Skeletal Muscle Female	skeletal muscle
16	chr1:222820800-222841200	Strong transcription	Fetal Intestine Large	intestine
17	chr1:222821000-222840000	Strong transcription	Fetal Kidney	kidney
18	chr1:222821200-222841400	Strong transcription	Adipose Nuclei	Adipose
19	chr1:222821400-222840000	Strong transcription	Fetal Brain Female	brain
20	chr1:222822200-222838800	Strong transcription	Colon Smooth Muscle	Colon
21	chr1:222822200-222841200	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr1:222822200-222841400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr1:222822400-222841200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:222822400-222841400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr1:222822600-222840000	Strong transcription	Fetal Muscle Trunk	muscle
26	chr1:222822600-222841400	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr1:222822600-222841400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr1:222822800-222840800	Strong transcription	Stomach Smooth Muscle	stomach
29	chr1:222823000-222838400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:222823000-222839200	Strong transcription	Fetal Muscle Leg	muscle
31	chr1:222823000-222841200	Strong transcription	H1 Cell Line	embryonic stem cell
32	chr1:222823000-222841400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr1:222823200-222840000	Strong transcription	Brain Substantia Nigra	brain
34	chr1:222823200-222840600	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr1:222823200-222841400	Strong transcription	HepG2	liver
36	chr1:222823200-222841400	Strong transcription	K562	blood
37	chr1:222823400-222841400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:222824000-222839600	Strong transcription	Skeletal Muscle Male	skeletal muscle
39	chr1:222824000-222841400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr1:222824000-222841400	Strong transcription	A549	lung
41	chr1:222824200-222839800	Strong transcription	Fetal Lung	lung
42	chr1:222825000-222841400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr1:222825200-222839000	Strong transcription	Brain Cingulate Gyrus	brain
44	chr1:222825600-222840000	Strong transcription	Left Ventricle	heart
45	chr1:222825800-222839600	Strong transcription	Rectal Smooth Muscle	rectum
46	chr1:222826800-222841400	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr1:222827000-222838000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr1:222827000-222845400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr1:222827200-222839000	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr1:222827400-222837600	Weak transcription	Pancreatic Islets	Pancreatic Islet

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