Variant report

Variant	rs6440420
Chromosome Location	chr3:145842403-145842404
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:145832521..145835172-chr3:145842139..145845404,4	MCF-7	breast:
2	chr3:145835695..145838592-chr3:145842329..145844265,2	MCF-7	breast:
3	chr3:145841734..145843545-chr3:145847343..145850022,2	MCF-7	breast:
4	chr3:145839176..145842654-chr3:145877605..145880673,5	MCF-7	breast:
5	chr3:145841131..145847641-chr3:145875218..145882802,13	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152952	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10935601	0.93[YRI][hapmap];0.86[AFR][1000 genomes]
rs10935602	0.87[AFR][1000 genomes]
rs11717610	0.81[AFR][1000 genomes]
rs11916662	1.00[AMR][1000 genomes]
rs11917712	1.00[AMR][1000 genomes]
rs11917774	1.00[AMR][1000 genomes]
rs11917816	1.00[AMR][1000 genomes]
rs11919826	1.00[AMR][1000 genomes]
rs11925421	1.00[AMR][1000 genomes]
rs12171307	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13087364	0.93[YRI][hapmap]
rs1375579	1.00[ASN][1000 genomes]
rs1375586	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1375589	0.90[YRI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1375591	0.92[YRI][hapmap];0.86[AFR][1000 genomes]
rs1512898	1.00[AMR][1000 genomes]
rs1512899	1.00[AMR][1000 genomes]
rs1530742	1.00[ASN][1000 genomes]
rs1982381	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1982382	0.92[YRI][hapmap]
rs2055978	1.00[AMR][1000 genomes]
rs2197907	0.86[EUR][1000 genomes]
rs2669397	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4681297	0.92[YRI][hapmap];0.89[AFR][1000 genomes]
rs55721145	1.00[AMR][1000 genomes]
rs56686359	0.81[AFR][1000 genomes]
rs57931335	1.00[AMR][1000 genomes]
rs59713697	1.00[AMR][1000 genomes]
rs6440412	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6440418	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6781300	0.93[YRI][hapmap];0.86[AFR][1000 genomes]
rs6783926	0.89[AFR][1000 genomes]
rs6792464	0.92[YRI][hapmap]
rs72989693	1.00[AMR][1000 genomes]
rs72996207	1.00[AMR][1000 genomes]
rs72996210	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72996212	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73865335	1.00[AMR][1000 genomes]
rs73865338	1.00[AMR][1000 genomes]
rs7613150	0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs7626859	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7639115	0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7642940	0.93[YRI][hapmap];0.86[AFR][1000 genomes]
rs895928	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9820945	0.92[YRI][hapmap];0.86[AFR][1000 genomes]
rs9830375	1.00[ASN][1000 genomes]
rs9836725	0.93[YRI][hapmap]
rs9869137	0.92[YRI][hapmap]
rs9869319	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9881770	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9881772	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525829	chr3:145614317-145863779	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv4046	chr3:145693249-145880189	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv877613	chr3:145833232-145912055	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145782800-145843200	Weak transcription	Pancreas	Pancrea
2	chr3:145784600-145848800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:145790400-145843200	Weak transcription	Right Ventricle	heart
4	chr3:145810400-145849800	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr3:145810800-145851200	Weak transcription	Brain Hippocampus Middle	brain
6	chr3:145819800-145849200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:145821000-145849800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr3:145827000-145855200	Weak transcription	Aorta	Aorta
9	chr3:145831400-145848400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr3:145832000-145870800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:145832600-145848400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:145833600-145843200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:145834200-145851200	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr3:145834400-145851400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr3:145834600-145852800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:145835200-145851200	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr3:145835200-145852200	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr3:145835600-145843600	Weak transcription	NHEK	skin
19	chr3:145835600-145851200	Weak transcription	Fetal Kidney	kidney
20	chr3:145835800-145843200	Weak transcription	Small Intestine	intestine
21	chr3:145835800-145846000	Weak transcription	Fetal Intestine Small	intestine
22	chr3:145835800-145874000	Weak transcription	Psoas Muscle	Psoas
23	chr3:145836000-145852400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr3:145836200-145844200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:145836800-145844000	Weak transcription	NHLF	lung
26	chr3:145837000-145843200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:145837000-145843200	Weak transcription	Esophagus	oesophagus
28	chr3:145837000-145844200	Weak transcription	NHDF-Ad	bronchial
29	chr3:145837000-145848800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr3:145837000-145852400	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr3:145837200-145845800	Weak transcription	Stomach Smooth Muscle	stomach
32	chr3:145837200-145846000	Weak transcription	Adipose Nuclei	Adipose
33	chr3:145837200-145846000	Weak transcription	Fetal Lung	lung
34	chr3:145837200-145851200	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr3:145838800-145843200	Strong transcription	HSMM	muscle
36	chr3:145839200-145845200	Weak transcription	Colon Smooth Muscle	Colon
37	chr3:145839400-145847600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr3:145839600-145844000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr3:145839800-145849000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr3:145839800-145851400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr3:145840000-145852400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr3:145840200-145842800	Weak transcription	Rectal Smooth Muscle	rectum
43	chr3:145840200-145847600	Weak transcription	HSMMtube	muscle
44	chr3:145840200-145849800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr3:145840400-145843200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr3:145840400-145843200	Weak transcription	NH-A	brain
47	chr3:145840400-145843800	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr3:145840400-145846000	Weak transcription	Fetal Intestine Large	intestine
49	chr3:145840400-145874000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr3:145840600-145843200	Weak transcription	Left Ventricle	heart

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