Variant report

Variant	rs2138374
Chromosome Location	chr2:190014317-190014318
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:190010189..190015498-chr2:190084856..190090227,6	MCF-7	breast:
2	chr2:190012942..190018195-chr2:190085147..190088368,4	MCF-7	breast:
3	chr2:190012335..190014833-chr2:190305566..190308252,2	K562	blood:
4	chr2:190011309..190014664-chr2:190015340..190018196,3	MCF-7	breast:
5	chr2:190009672..190012022-chr2:190013426..190016252,2	K562	blood:

Variant related genes	Relation type
ENSG00000115368	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10931400	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10931404	0.82[EUR][1000 genomes]
rs11681286	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11691604	0.81[JPT][hapmap]
rs12104769	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12105389	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12611950	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12615823	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12618438	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12621035	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12621806	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12621939	0.86[EUR][1000 genomes]
rs12991770	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12993719	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12995956	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12999122	0.87[EUR][1000 genomes]
rs12999996	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13004722	0.85[EUR][1000 genomes]
rs13005652	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13005714	0.85[YRI][hapmap]
rs13005821	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13011374	0.87[EUR][1000 genomes]
rs13011485	0.86[EUR][1000 genomes]
rs13012327	0.82[EUR][1000 genomes]
rs13012649	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13015283	0.84[CEU][hapmap];0.81[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13016231	0.87[EUR][1000 genomes]
rs13017413	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13019076	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13020999	0.87[YRI][hapmap]
rs13021508	0.86[EUR][1000 genomes]
rs13022633	0.88[EUR][1000 genomes]
rs13028967	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13029705	0.92[EUR][1000 genomes]
rs13030984	0.85[YRI][hapmap]
rs13031211	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13031549	0.85[CEU][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs13033421	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1356162	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1356163	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1356164	0.92[CEU][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1356165	0.92[CEU][hapmap];0.81[JPT][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1356167	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1356168	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1399991	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1399992	0.82[EUR][1000 genomes]
rs1464135	0.80[YRI][hapmap]
rs1515864	0.87[YRI][hapmap]
rs1515874	0.82[EUR][1000 genomes]
rs1515876	0.82[EUR][1000 genomes]
rs1568334	0.86[EUR][1000 genomes]
rs1878085	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1949327	0.85[YRI][hapmap]
rs1949484	0.87[EUR][1000 genomes]
rs1965422	0.89[CEU][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2138373	0.83[YRI][hapmap]
rs2222256	0.87[EUR][1000 genomes]
rs2351627	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2351636	0.85[EUR][1000 genomes]
rs35475196	0.82[EUR][1000 genomes]
rs3914778	0.87[EUR][1000 genomes]
rs4233801	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4417749	0.85[YRI][hapmap]
rs4428040	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4667264	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4667265	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4667272	0.87[EUR][1000 genomes]
rs4667274	0.90[EUR][1000 genomes]
rs4667276	0.86[EUR][1000 genomes]
rs4667277	0.86[EUR][1000 genomes]
rs4998559	0.92[CEU][hapmap];0.81[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs60124911	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs62182416	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6434324	0.84[YRI][hapmap]
rs6434339	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs6708419	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6714088	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6719104	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6737071	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6749559	0.87[YRI][hapmap]
rs7419888	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7560973	0.87[YRI][hapmap]
rs7561002	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7564611	0.88[EUR][1000 genomes]
rs7576165	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs7587147	0.87[EUR][1000 genomes]
rs7587956	0.87[EUR][1000 genomes]
rs7607133	0.90[EUR][1000 genomes]
rs7609495	0.82[EUR][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	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv875613	chr2:189999011-190324685	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189981400-190014800	Weak transcription	Fetal Stomach	stomach
2	chr2:189984000-190016800	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr2:189993800-190017000	Weak transcription	Ovary	ovary
4	chr2:190003600-190014600	Weak transcription	Colon Smooth Muscle	Colon
5	chr2:190008000-190014800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:190009000-190016000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr2:190009200-190014400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:190009400-190014800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:190009600-190014800	Weak transcription	Aorta	Aorta
10	chr2:190009800-190014600	Weak transcription	NH-A	brain
11	chr2:190009800-190017200	Weak transcription	Fetal Muscle Leg	muscle
12	chr2:190011000-190014800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr2:190011200-190020800	Enhancers	NHDF-Ad	bronchial
14	chr2:190011600-190016200	Weak transcription	Fetal Lung	lung
15	chr2:190012000-190014600	Weak transcription	NHLF	lung
16	chr2:190012200-190016800	Weak transcription	HSMMtube	muscle
17	chr2:190012400-190018000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr2:190012600-190017200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr2:190013200-190014600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr2:190013200-190017000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr2:190013600-190015000	Enhancers	HSMM	muscle
22	chr2:190013600-190017200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:190013800-190014400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr2:190013800-190014600	Enhancers	A549	lung
25	chr2:190013800-190015000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr2:190013800-190015200	Enhancers	Adipose Nuclei	Adipose
27	chr2:190014000-190016800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:190014200-190014600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr2:190014200-190015600	Enhancers	Hela-S3	cervix
30	chr2:190014200-190016000	Enhancers	Muscle Satellite Cultured Cells	--
31	chr2:190014200-190016800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr2:190014200-190017200	Enhancers	Osteobl	bone

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