Variant report

Variant	rs2854394
Chromosome Location	chr3:48621593-48621594
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:48595024..48597915-chr3:48619806..48622273,2	K562	blood:
2	chr3:48620158..48621979-chr3:48670195..48672558,2	K562	blood:

Variant related genes	Relation type
ENSG00000225697	Chromatin interaction
ENSG00000114268	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1003649	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.83[ASN][1000 genomes]
rs10470687	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11706983	0.83[GIH][hapmap]
rs11708786	0.83[GIH][hapmap]
rs11719291	0.83[GIH][hapmap]
rs12107252	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs12107418	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs13060933	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13062576	1.00[CEU][hapmap]
rs13063312	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs13070798	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs13091944	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[ASN][1000 genomes]
rs13319635	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13319651	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.88[TSI][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13324142	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs13434258	0.83[GIH][hapmap]
rs17080289	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2006871	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2255532	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs2276850	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2276852	0.80[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2286652	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2302295	1.00[JPT][hapmap]
rs2310996	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2854395	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28563843	0.88[ASN][1000 genomes]
rs28581474	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34107861	0.85[CHD][hapmap]
rs35064573	0.83[GIH][hapmap]
rs35343040	0.92[ASN][1000 genomes]
rs35562294	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35796820	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3755819	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3806694	1.00[JPT][hapmap]
rs3821875	1.00[JPT][hapmap]
rs3821876	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs3969942	0.85[CHD][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap]
rs6773261	1.00[JPT][hapmap]
rs6781283	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6792156	1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6792525	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6806059	0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs740787	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs7428949	1.00[JPT][hapmap]
rs7434077	0.80[CHD][hapmap]
rs7620853	1.00[JPT][hapmap]
rs7631574	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9810549	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9810991	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9811318	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9812200	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9814951	0.80[CHB][hapmap];0.85[GIH][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs9821797	1.00[JPT][hapmap]
rs9830581	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9835902	0.85[GIH][hapmap];0.81[TSI][hapmap]
rs9836462	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9837687	0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9841602	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9843316	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9848824	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9849280	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9850102	0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.86[ASN][1000 genomes]
rs9851771	0.80[CHD][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap]
rs9864729	0.88[ASN][1000 genomes]
rs9869698	0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs9871180	0.90[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9873726	1.00[JPT][hapmap]
rs9875911	1.00[GIH][hapmap]
rs9878950	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9881877	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.92[ASN][1000 genomes]
rs9882549	0.83[GIH][hapmap]
rs9882962	0.85[CHD][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008232	chr3:48517121-48702416	Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv523981	chr3:48520289-48721040	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1004383	chr3:48543794-48649772	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv876762	chr3:48591481-48731487	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv3811	chr3:48599180-48643809	Enhancers Genic enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv818138	chr3:48610925-48731487	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
8	nsv933568	chr3:48620655-48623089	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv933666	chr3:48621036-48622669	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48596600-48626000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:48598600-48624000	Weak transcription	Aorta	Aorta
3	chr3:48599000-48623600	Weak transcription	Ovary	ovary
4	chr3:48599000-48632000	Weak transcription	Left Ventricle	heart
5	chr3:48599200-48630600	Weak transcription	Duodenum Mucosa	Duodenum
6	chr3:48600600-48631800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr3:48601000-48631000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
8	chr3:48601600-48631000	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr3:48601800-48633000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:48602000-48629400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:48602000-48633200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:48602200-48629400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:48603600-48630000	Strong transcription	Fetal Stomach	stomach
14	chr3:48603800-48628800	Strong transcription	Placenta Amnion	Placenta Amnion
15	chr3:48603800-48630600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr3:48603800-48631800	Weak transcription	Gastric	stomach
17	chr3:48604000-48623800	Weak transcription	Fetal Muscle Leg	muscle
18	chr3:48604000-48629400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr3:48604000-48631600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:48604000-48632000	Weak transcription	HSMMtube	muscle
21	chr3:48604200-48621600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr3:48604400-48630000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:48604400-48631600	Weak transcription	HSMM	muscle
24	chr3:48604600-48630800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:48605000-48627400	Strong transcription	NHEK	skin
26	chr3:48606200-48627600	Strong transcription	HMEC	breast
27	chr3:48606800-48627000	Strong transcription	A549	lung
28	chr3:48607400-48623800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr3:48607600-48622200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr3:48610200-48631200	Strong transcription	Fetal Intestine Small	intestine
31	chr3:48610800-48626000	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr3:48611800-48624000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr3:48613400-48621600	Strong transcription	Stomach Smooth Muscle	stomach
34	chr3:48613800-48622200	Weak transcription	Fetal Brain Female	brain
35	chr3:48615200-48627200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:48615200-48629600	Weak transcription	Brain Substantia Nigra	brain
37	chr3:48615200-48632000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr3:48615200-48632200	Weak transcription	Brain Anterior Caudate	brain
39	chr3:48615400-48623800	Weak transcription	Brain Angular Gyrus	brain
40	chr3:48615400-48625600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr3:48615800-48623400	Weak transcription	Spleen	Spleen
42	chr3:48616000-48623200	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr3:48616600-48624200	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr3:48616800-48624200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr3:48617000-48631600	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr3:48617200-48630200	Weak transcription	NHDF-Ad	bronchial
47	chr3:48617600-48622000	Strong transcription	Fetal Intestine Large	intestine
48	chr3:48617800-48622800	Weak transcription	NHLF	lung
49	chr3:48618400-48627000	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr3:48618600-48622800	Weak transcription	Skeletal Muscle Male	skeletal muscle

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