Variant report

Variant	rs13022800
Chromosome Location	chr2:173970922-173970923
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:173939636..173941560-chr2:173969375..173971001,2	MCF-7	breast:
2	chr2:173969673..173972260-chr2:173985916..173987500,2	MCF-7	breast:
3	chr2:173965020..173969595-chr2:173970768..173975249,5	K562	blood:

Variant related genes	Relation type
ENSG00000091436	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs12986917	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12987496	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12989116	0.91[CHB][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12997078	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs13004212	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13017210	0.84[ASN][1000 genomes]
rs13020796	0.82[ASN][1000 genomes]
rs13029949	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap]
rs13032010	0.92[CHB][hapmap]
rs16861272	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16861278	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs17302977	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17761169	0.92[CHB][hapmap];0.85[ASN][1000 genomes]
rs2278883	0.88[CEU][hapmap];0.91[CHB][hapmap];0.87[ASN][1000 genomes]
rs2289397	0.83[CHB][hapmap]
rs2289399	0.90[CHB][hapmap]
rs34014656	0.87[ASN][1000 genomes]
rs34472765	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34658268	0.83[ASN][1000 genomes]
rs34681024	0.91[ASN][1000 genomes]
rs34702663	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35250703	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36102078	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3754741	0.90[CHB][hapmap]
rs3754743	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap]
rs3754744	0.90[CHB][hapmap];1.00[YRI][hapmap]
rs3769161	0.81[CHB][hapmap]
rs3769167	0.91[CHB][hapmap]
rs3769187	0.92[CHB][hapmap]
rs3769192	0.91[CEU][hapmap];0.90[CHB][hapmap]
rs3769194	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs3769199	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3769203	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4972533	0.90[CHB][hapmap]
rs56193548	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56342397	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6433395	0.84[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6741675	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67422536	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67683956	0.83[ASN][1000 genomes]
rs72905046	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72905080	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011724	chr2:173916482-174231908	Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv834460	chr2:173919464-174085288	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173942800-173971400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr2:173943000-173971200	Weak transcription	HSMMtube	muscle
3	chr2:173943400-173974200	Weak transcription	Fetal Intestine Large	intestine
4	chr2:173945400-173991200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr2:173952000-173973400	Weak transcription	Hela-S3	cervix
6	chr2:173952200-173971400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr2:173953800-173991400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr2:173955600-173971800	Weak transcription	Lung	lung
9	chr2:173955600-173972000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:173955600-173984000	Weak transcription	Gastric	stomach
11	chr2:173955800-173977200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr2:173956600-173971600	Weak transcription	Fetal Thymus	thymus
13	chr2:173957000-173974400	Weak transcription	Fetal Stomach	stomach
14	chr2:173957600-173972000	Weak transcription	Fetal Muscle Trunk	muscle
15	chr2:173957800-173973400	Weak transcription	Fetal Lung	lung
16	chr2:173957800-173983800	Weak transcription	Fetal Muscle Leg	muscle
17	chr2:173958000-173983800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:173958200-173973800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr2:173958200-173974000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr2:173959800-173974200	Weak transcription	HepG2	liver
21	chr2:173961400-173973400	Weak transcription	Fetal Intestine Small	intestine
22	chr2:173961800-173974400	Weak transcription	NHLF	lung
23	chr2:173962000-173971000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:173962200-173983800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:173964600-173971200	Weak transcription	HSMM	muscle
26	chr2:173964600-173971600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr2:173965000-173974000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr2:173965000-173987400	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr2:173965400-173971400	Weak transcription	HMEC	breast
30	chr2:173965400-173984400	Weak transcription	Aorta	Aorta
31	chr2:173965400-173987200	Weak transcription	Dnd41	blood
32	chr2:173965400-173989200	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr2:173965600-173971000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr2:173965600-173973800	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr2:173965600-173983800	Weak transcription	Adipose Nuclei	Adipose
36	chr2:173966800-173971000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:173966800-173971200	Weak transcription	A549	lung
38	chr2:173966800-173973800	Weak transcription	NHEK	skin
39	chr2:173967000-173972600	Weak transcription	Osteobl	bone
40	chr2:173967200-173971200	Weak transcription	Liver	Liver
41	chr2:173967200-173971400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr2:173967200-173973200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:173967200-173973200	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr2:173967600-173971200	Weak transcription	Colon Smooth Muscle	Colon
45	chr2:173967600-173971200	Weak transcription	Ovary	ovary
46	chr2:173967600-173973800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr2:173968000-173971600	Weak transcription	K562	blood
48	chr2:173968200-173974600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr2:173968600-173973600	Weak transcription	GM12878-XiMat	blood
50	chr2:173968600-173990600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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