Variant report

Variant	rs10202823
Chromosome Location	chr2:172780132-172780133
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:172777448..172780686-chr2:172863264..172866650,5	K562	blood:
2	chr2:172690324..172692535-chr2:172778951..172781144,3	K562	blood:
3	chr2:172779934..172782820-chr2:172786897..172788575,2	MCF-7	breast:
4	chr2:172779206..172781039-chr2:172947710..172950652,2	K562	blood:
5	chr2:172776261..172781039-chr2:172946394..172953961,9	K562	blood:
6	chr2:172777519..172781580-chr2:172819100..172823049,4	K562	blood:
7	chr2:172778049..172781927-chr2:172965294..172970550,9	K562	blood:
8	chr2:172777448..172780536-chr2:172864307..172867165,5	K562	blood:
9	chr2:172777989..172784973-chr2:172962042..172968003,11	K562	blood:
10	chr2:172749385..172752362-chr2:172779098..172783248,3	MCF-7	breast:
11	chr2:172749065..172752809-chr2:172776821..172780584,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000236651	Chromatin interaction
ENSG00000115840	Chromatin interaction
ENSG00000115844	Chromatin interaction
ENSG00000128708	Chromatin interaction
ENSG00000144355	Chromatin interaction
ENSG00000172878	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10165126	0.88[CEU][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap]
rs10166548	0.89[AMR][1000 genomes]
rs10167419	0.87[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs10174055	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10194102	0.87[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs10200608	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs10201430	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10207085	0.87[CEU][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs10930502	0.87[CEU][hapmap]
rs11757	0.87[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs11904009	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs12692973	0.87[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.81[MKK][hapmap]
rs12692974	0.87[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs12692978	0.83[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.83[MKK][hapmap]
rs13004237	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13017585	0.92[ASW][hapmap];0.84[GIH][hapmap]
rs13030911	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2165934	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2292815	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs3770445	0.83[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.83[MKK][hapmap]
rs3770451	0.87[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.80[MKK][hapmap]
rs3770452	0.87[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[MKK][hapmap]
rs4667694	0.92[ASW][hapmap];0.87[CEU][hapmap];0.92[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap]
rs4668414	1.00[ASW][hapmap];0.87[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.86[MKK][hapmap]
rs62182433	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6433319	1.00[CEU][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6710698	0.83[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs6715929	0.96[CEU][hapmap];0.87[TSI][hapmap]
rs6722757	0.85[ASW][hapmap];0.87[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs6724337	0.87[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap];0.83[MKK][hapmap]
rs6725388	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs6727017	0.96[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6731562	1.00[CEU][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6738445	0.83[CEU][hapmap];0.86[JPT][hapmap]
rs6745143	0.87[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[MKK][hapmap]
rs6750058	0.86[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6752812	0.91[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.88[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6754817	1.00[ASW][hapmap];0.87[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs6758704	0.87[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[MKK][hapmap]
rs6759575	0.87[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.83[MKK][hapmap]
rs7563971	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7564089	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7573003	0.87[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs7581072	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7586207	0.87[CEU][hapmap];0.81[CHB][hapmap];0.96[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs7602037	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7608403	0.87[CEU][hapmap];0.81[CHB][hapmap];0.92[CHD][hapmap];0.80[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap]
rs908670	0.83[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.83[MKK][hapmap]
rs908671	0.83[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875410	chr2:172693780-172896587	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv875411	chr2:172693780-172942448	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv536037	chr2:172745597-172780616	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs10202823	MAP1D	cis	parietal	SCAN
rs10202823	AC068039.4	cis	Esophagus Muscularis	GTEx
rs10202823	MYO3B	cis	cerebellum	SCAN
rs10202823	SLC25A12	cis	cerebellum	SCAN
rs10202823	AC068039.4	cis	Adipose Subcutaneous	GTEx
rs10202823	AC068039.4	cis	Skin Sun Exposed Lower leg	GTEx
rs10202823	PDK1	cis	cerebellum	SCAN
rs10202823	SLC25A12	Cis_1M	lymphoblastoid	RTeQTL
rs10202823	AC068039.4	cis	Whole Blood	GTEx
rs10202823	AC068039.4	cis	Esophagus Mucosa	GTEx
rs10202823	AC068039.4	cis	lung	GTEx
rs10202823	DYNC1I2	cis	lymphoblastoid	seeQTL
rs10202823	SLC25A12	cis	parietal	SCAN
rs10202823	DYNC1I2	cis	cerebellum	SCAN
rs10202823	AC068039.4	cis	Heart Left Ventricle	GTEx
rs10202823	AC068039.4	cis	Stomach	GTEx
rs10202823	AC068039.4	cis	Thyroid	GTEx
rs10202823	AC068039.4	cis	Nerve Tibial	GTEx
rs10202823	AC068039.4	cis	Muscle Skeletal	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172778400-172780200	Active TSS	H9 Cell Line	embryonic stem cell
2	chr2:172778400-172780200	Active TSS	Ovary	ovary
3	chr2:172778400-172780200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
4	chr2:172778400-172780400	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr2:172778400-172780400	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr2:172778400-172780400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:172778400-172780400	Active TSS	Right Atrium	heart
8	chr2:172778400-172780800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr2:172778600-172780200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr2:172778600-172780200	Active TSS	Pancreas	Pancrea
11	chr2:172778600-172780200	Active TSS	Hela-S3	cervix
12	chr2:172778600-172780800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr2:172778800-172780200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr2:172778800-172780400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:172778800-172780400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr2:172779200-172780200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
17	chr2:172779200-172780400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr2:172779200-172780600	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr2:172779200-172780800	Flanking Active TSS	Primary hematopoietic stem cells	blood
20	chr2:172779200-172781600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr2:172779400-172780200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
22	chr2:172779400-172780200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
23	chr2:172779400-172780200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
24	chr2:172779400-172780400	Flanking Active TSS	Primary T cells from cord blood	blood
25	chr2:172779400-172780400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
26	chr2:172779400-172780400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
27	chr2:172779400-172780400	Flanking Active TSS	Rectal Smooth Muscle	rectum
28	chr2:172779400-172780400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr2:172779400-172780400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
30	chr2:172779400-172780600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:172779400-172781000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr2:172779600-172780200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr2:172779600-172780200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
34	chr2:172779600-172780200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
35	chr2:172779600-172780200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
36	chr2:172779600-172780200	Flanking Active TSS	Adipose Nuclei	Adipose
37	chr2:172779600-172780200	Flanking Active TSS	Liver	Liver
38	chr2:172779600-172780200	Flanking Active TSS	Fetal Brain Male	brain
39	chr2:172779600-172780400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr2:172779600-172780400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr2:172779600-172780400	Flanking Active TSS	Thymus	Thymus
42	chr2:172779600-172780600	Flanking Active TSS	Fetal Heart	heart
43	chr2:172779600-172780800	Flanking Active TSS	Brain Germinal Matrix	brain
44	chr2:172779600-172784600	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr2:172779800-172780200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr2:172779800-172780200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr2:172779800-172780200	Flanking Active TSS	Brain Anterior Caudate	brain
48	chr2:172779800-172780200	Flanking Active TSS	Brain Cingulate Gyrus	brain
49	chr2:172779800-172780200	Flanking Active TSS	Brain Hippocampus Middle	brain
50	chr2:172779800-172780200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain

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