Variant report

Variant	rs3821841
Chromosome Location	chr3:52084040-52084041
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52081717..52084424-chr3:52095750..52098933,3	K562	blood:
2	chr3:52063502..52067953-chr3:52083827..52087506,5	K562	blood:
3	chr3:52035106..52036016-chr3:52083953..52084656,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256097	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12485855	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12488456	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12489539	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12492696	0.83[AMR][1000 genomes]
rs12493204	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13096104	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13316105	0.83[AMR][1000 genomes]
rs17051963	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2334959	0.82[AMR][1000 genomes]
rs2334960	0.81[AMR][1000 genomes]
rs4687606	0.83[AMR][1000 genomes]
rs4687608	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs4687609	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4687798	0.86[MEX][hapmap];0.82[AMR][1000 genomes]
rs4687799	0.82[AMR][1000 genomes]
rs4687801	0.85[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4687802	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4687806	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4687808	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4687809	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs66530305	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6792935	0.82[AMR][1000 genomes]
rs72622936	0.82[AMR][1000 genomes]
rs72622937	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs745618	0.82[AMR][1000 genomes]
rs7618573	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs920160	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9637473	0.92[EUR][1000 genomes]
rs9873175	0.91[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1003453	chr3:51962081-52099441	Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	esv1804090	chr3:51962081-52140591	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
4	esv1835339	chr3:51962081-52140591	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	nsv1003581	chr3:51973395-52108645	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	nsv1001062	chr3:51973395-52134638	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	nsv876780	chr3:51981021-52101799	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
9	nsv876786	chr3:52041566-52236762	Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
11	esv1792042	chr3:52070955-52091254	Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
12	esv1793040	chr3:52070955-52091254	Active TSS Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
13	esv1797975	chr3:52070955-52091254	Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
14	esv1798814	chr3:52070955-52091254	Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
15	esv1797189	chr3:52070955-52101799	Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
16	esv1798365	chr3:52070955-52101799	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
17	nsv963319	chr3:52082531-52085712	Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52076000-52086400	Weak transcription	Fetal Brain Male	brain
2	chr3:52078200-52084200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:52078600-52084200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:52079800-52085000	Weak transcription	K562	blood
5	chr3:52080800-52085000	Weak transcription	GM12878-XiMat	blood
6	chr3:52081200-52086600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr3:52081400-52085200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr3:52081400-52085800	Strong transcription	Thymus	Thymus
9	chr3:52081400-52086400	Weak transcription	Psoas Muscle	Psoas
10	chr3:52081600-52085400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr3:52081600-52085600	Strong transcription	Fetal Intestine Small	intestine
12	chr3:52081600-52088600	Genic enhancers	Placenta	Placenta
13	chr3:52081600-52088800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr3:52081800-52084800	Genic enhancers	NHEK	skin
15	chr3:52081800-52085200	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr3:52081800-52085800	Genic enhancers	Brain Anterior Caudate	brain
17	chr3:52081800-52086000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
18	chr3:52081800-52086200	Strong transcription	Fetal Brain Female	brain
19	chr3:52081800-52086600	Genic enhancers	Right Ventricle	heart
20	chr3:52081800-52086800	Genic enhancers	Lung	lung
21	chr3:52081800-52088200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:52082000-52084200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr3:52082000-52084800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr3:52082000-52085000	Weak transcription	HSMM	muscle
25	chr3:52082000-52085400	Weak transcription	HepG2	liver
26	chr3:52082000-52086000	Weak transcription	Fetal Heart	heart
27	chr3:52082000-52086200	Genic enhancers	Brain Inferior Temporal Lobe	brain
28	chr3:52082000-52086200	Weak transcription	HSMMtube	muscle
29	chr3:52082000-52086600	Weak transcription	A549	lung
30	chr3:52082200-52085200	Strong transcription	Rectal Smooth Muscle	rectum
31	chr3:52082200-52085400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
32	chr3:52082200-52085600	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr3:52082200-52085600	Genic enhancers	Primary T cells fromperipheralblood	blood
34	chr3:52082200-52085800	Genic enhancers	Brain Hippocampus Middle	brain
35	chr3:52082200-52086200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
36	chr3:52082200-52086200	Genic enhancers	Stomach Smooth Muscle	stomach
37	chr3:52082200-52086400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr3:52082200-52086800	Strong transcription	Brain Germinal Matrix	brain
39	chr3:52082400-52084200	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr3:52082400-52084600	Weak transcription	Fetal Kidney	kidney
41	chr3:52082400-52085200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr3:52082400-52085200	Strong transcription	Fetal Thymus	thymus
43	chr3:52082400-52085400	Genic enhancers	Brain Substantia Nigra	brain
44	chr3:52082400-52085600	Genic enhancers	HMEC	breast
45	chr3:52082400-52086000	Genic enhancers	Brain Cingulate Gyrus	brain
46	chr3:52082400-52086000	Genic enhancers	Left Ventricle	heart
47	chr3:52082400-52086200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr3:52082400-52086800	Genic enhancers	Esophagus	oesophagus
49	chr3:52082400-52088000	Strong transcription	Fetal Intestine Large	intestine
50	chr3:52082400-52088000	Genic enhancers	Spleen	Spleen

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