Variant report

Variant	rs1003649
Chromosome Location	chr3:48618666-48618667
allele	A/G
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	POLR2A	chr3:48618075-48619031	Hela-S3	cervix:	n/a	n/a
2	ZBTB7A	chr3:48618619-48618777	K562	blood:	n/a	n/a
3	POLR2A	chr3:48618590-48618764	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:48618345..48620627-chr3:48630750..48633502,2	K562	blood:
2	chr3:48617868..48620295-chr3:48645648..48648360,2	MCF-7	breast:

Variant related genes	Relation type
MIR711	TF binding region
ENSG00000114270	Chromatin interaction
ENSG00000010256	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10470687	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes]
rs11706983	0.83[GIH][hapmap]
rs11708786	0.83[GIH][hapmap]
rs11719291	0.83[GIH][hapmap]
rs12107252	0.83[GIH][hapmap]
rs12107418	0.83[GIH][hapmap]
rs13060933	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap]
rs13063312	0.83[GIH][hapmap]
rs13070798	0.83[GIH][hapmap]
rs13091944	0.90[CHB][hapmap]
rs13319651	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap]
rs13324142	0.83[GIH][hapmap]
rs13434258	0.83[GIH][hapmap]
rs17080289	1.00[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap]
rs2006871	0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap]
rs2255532	0.82[CHB][hapmap]
rs2276850	0.83[GIH][hapmap]
rs2276852	0.83[GIH][hapmap]
rs2286652	0.83[GIH][hapmap]
rs2310996	0.83[GIH][hapmap]
rs2854394	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.83[ASN][1000 genomes]
rs2854395	0.83[ASN][1000 genomes]
rs28581474	0.81[ASN][1000 genomes]
rs35064573	0.83[GIH][hapmap]
rs35343040	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3821876	0.83[GIH][hapmap]
rs3969942	0.80[CHD][hapmap];1.00[GIH][hapmap]
rs6781283	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap]
rs6792156	1.00[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes]
rs6792525	0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.81[TSI][hapmap];0.85[YRI][hapmap]
rs6806059	0.90[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap]
rs740787	0.83[GIH][hapmap]
rs7631574	0.83[GIH][hapmap]
rs9810549	0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap]
rs9810991	0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.81[TSI][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes]
rs9811318	0.83[GIH][hapmap]
rs9812200	0.83[GIH][hapmap]
rs9814951	0.80[CHB][hapmap];0.85[GIH][hapmap]
rs9830581	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap]
rs9835902	0.85[GIH][hapmap]
rs9836462	0.83[GIH][hapmap]
rs9837687	0.90[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap]
rs9841602	0.83[GIH][hapmap]
rs9843316	1.00[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap]
rs9850102	0.90[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap]
rs9851771	1.00[GIH][hapmap]
rs9869698	0.90[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.80[LWK][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes]
rs9871180	0.90[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap]
rs9875911	1.00[GIH][hapmap]
rs9878950	0.86[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs9881877	1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.87[LWK][hapmap];0.88[MEX][hapmap];0.86[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs9882549	0.83[GIH][hapmap]
rs9882962	0.80[CHD][hapmap];1.00[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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

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	chr3:48602000-48619400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:48602000-48629400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:48602000-48633200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr3:48602200-48629400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr3:48602400-48621400	Weak transcription	Brain Hippocampus Middle	brain
15	chr3:48603600-48630000	Strong transcription	Fetal Stomach	stomach
16	chr3:48603800-48628800	Strong transcription	Placenta Amnion	Placenta Amnion
17	chr3:48603800-48630600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr3:48603800-48631800	Weak transcription	Gastric	stomach
19	chr3:48604000-48623800	Weak transcription	Fetal Muscle Leg	muscle
20	chr3:48604000-48629400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr3:48604000-48631600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:48604000-48632000	Weak transcription	HSMMtube	muscle
23	chr3:48604200-48621600	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr3:48604400-48630000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:48604400-48631600	Weak transcription	HSMM	muscle
26	chr3:48604600-48630800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:48605000-48627400	Strong transcription	NHEK	skin
28	chr3:48606200-48627600	Strong transcription	HMEC	breast
29	chr3:48606800-48627000	Strong transcription	A549	lung
30	chr3:48607400-48623800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:48607600-48622200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr3:48608000-48619800	Strong transcription	NH-A	brain
33	chr3:48610200-48631200	Strong transcription	Fetal Intestine Small	intestine
34	chr3:48610800-48626000	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr3:48611800-48624000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:48612400-48618800	Weak transcription	HepG2	liver
37	chr3:48613000-48621200	Strong transcription	Right Ventricle	heart
38	chr3:48613400-48621600	Strong transcription	Stomach Smooth Muscle	stomach
39	chr3:48613800-48622200	Weak transcription	Fetal Brain Female	brain
40	chr3:48614200-48620600	Strong transcription	Hela-S3	cervix
41	chr3:48615200-48621400	Weak transcription	Brain Cingulate Gyrus	brain
42	chr3:48615200-48627200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr3:48615200-48629600	Weak transcription	Brain Substantia Nigra	brain
44	chr3:48615200-48632000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:48615200-48632200	Weak transcription	Brain Anterior Caudate	brain
46	chr3:48615400-48619400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr3:48615400-48623800	Weak transcription	Brain Angular Gyrus	brain
48	chr3:48615400-48625600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr3:48615800-48623400	Weak transcription	Spleen	Spleen
50	chr3:48616000-48623200	Weak transcription	HUES64 Cell Line	embryonic stem cell

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