Variant report

Variant	rs1878200
Chromosome Location	chr2:189836678-189836679
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr2:189836097-189836844	SK-N-SH	brain:	n/a	n/a
2	PBX3	chr2:189836253-189836771	SK-N-SH	brain:	n/a	n/a
3	GATA3	chr2:189836136-189836734	SK-N-SH	brain:	n/a	n/a
4	EP300	chr2:189836124-189836700	SK-N-SH	brain:	n/a	n/a
5	TCF12	chr2:189835993-189836858	SK-N-SH	brain:	n/a	n/a
6	GATA3	chr2:189836028-189836866	SK-N-SH	brain:	n/a	n/a
7	EP300	chr2:189836296-189836688	SK-N-SH_RA	brain:	n/a	n/a
8	EP300	chr2:189836295-189836685	SK-N-SH_RA	brain:	n/a	n/a

Variant related genes	Relation type
COL3A1	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10208496	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1040186	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12618257	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12693519	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12693520	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12693522	0.88[ASN][1000 genomes]
rs12693523	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12693524	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12990937	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13023280	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1516443	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1878199	1.00[ASN][1000 genomes]
rs2138533	0.96[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2351418	0.88[ASN][1000 genomes]
rs4667254	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6434304	0.87[ASN][1000 genomes]
rs6434305	1.00[ASN][1000 genomes]
rs7426072	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7603905	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834490	chr2:189703550-189840963	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv875608	chr2:189753823-189837995	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	esv1849974	chr2:189796272-189837995	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv584056	chr2:189796272-189841052	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv459992	chr2:189796272-189855943	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
6	nsv584057	chr2:189796272-189855943	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
7	nsv875609	chr2:189796272-189862097	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv875610	chr2:189796272-189904674	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv875611	chr2:189799499-189837212	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv584058	chr2:189799499-189855943	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
11	esv1791841	chr2:189811074-189864582	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
12	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

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189828400-189838400	Weak transcription	Fetal Kidney	kidney
2	chr2:189830800-189839000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr2:189833600-189836800	Enhancers	Fetal Lung	lung
4	chr2:189834200-189838600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr2:189834200-189838800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:189834200-189842800	Weak transcription	A549	lung
7	chr2:189834400-189838200	Weak transcription	Fetal Muscle Leg	muscle
8	chr2:189834800-189837200	Enhancers	Adipose Nuclei	Adipose
9	chr2:189835000-189836800	Enhancers	Placenta Amnion	Placenta Amnion
10	chr2:189835400-189838800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr2:189835400-189839200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:189835800-189838200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr2:189836200-189836800	Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr2:189836200-189837400	Enhancers	Fetal Stomach	stomach
15	chr2:189836200-189838400	Enhancers	Rectal Smooth Muscle	rectum
16	chr2:189836200-189839000	Weak transcription	Esophagus	oesophagus
17	chr2:189836400-189836800	Flanking Active TSS	Colon Smooth Muscle	Colon
18	chr2:189836400-189836800	Flanking Active TSS	Stomach Smooth Muscle	stomach
19	chr2:189836400-189837800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:189836400-189837800	Weak transcription	NHLF	lung
21	chr2:189836400-189838400	Weak transcription	HSMMtube	muscle
22	chr2:189836600-189836800	Enhancers	Small Intestine	intestine
23	chr2:189836600-189837200	Enhancers	NHDF-Ad	bronchial
24	chr2:189836600-189837800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr2:189836600-189837800	Weak transcription	Osteobl	bone
26	chr2:189836600-189838000	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr2:189836600-189838400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:189836600-189838400	Weak transcription	Ovary	ovary
29	chr2:189836600-189838400	Weak transcription	HSMM	muscle

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