Variant report

Variant	rs10456097
Chromosome Location	chr6:38000709-38000710
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:37786371..37788627-chr6:37999131..38001315,2	MCF-7	breast:
2	chr6:37983748..37986719-chr6:38000048..38002009,3	K562	blood:
3	chr6:37786481..37789207-chr6:38000677..38002350,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225945	Chromatin interaction
ENSG00000156639	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10947712	0.81[EUR][1000 genomes]
rs10947713	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1187422	0.84[ASN][1000 genomes]
rs1187423	0.84[ASN][1000 genomes]
rs12190306	0.83[EUR][1000 genomes]
rs12192182	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12194618	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12194823	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12198907	0.84[ASN][1000 genomes]
rs12200258	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12204352	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12206818	0.84[ASN][1000 genomes]
rs12211248	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12211981	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12212723	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12213151	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12213835	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12214375	0.82[EUR][1000 genomes]
rs13210701	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13214465	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13220131	0.92[EUR][1000 genomes]
rs16890344	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs171831	0.80[ASN][1000 genomes]
rs1812599	0.81[EUR][1000 genomes]
rs2132597	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs259673	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs259684	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs259686	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs259689	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs259690	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs259691	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs259695	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs259713	0.84[ASN][1000 genomes]
rs259715	0.84[ASN][1000 genomes]
rs259716	0.80[ASN][1000 genomes]
rs2645102	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2645107	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2645113	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2645116	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2645120	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2645127	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2645128	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2645131	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2645134	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2645137	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2842500	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2842517	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2842527	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2842529	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34871463	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35823566	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56098839	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56140804	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7747130	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs941850	0.82[EUR][1000 genomes]
rs9647619	0.84[ASN][1000 genomes]
rs966705	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1017051	chr6:37789341-38084719	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv538203	chr6:37789341-38084719	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1020625	chr6:37833591-38155622	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	esv34450	chr6:37963308-38007241	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	esv2763549	chr6:37985025-38014006	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv2754649	chr6:37985025-38147910	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37985000-38002400	Weak transcription	Primary B cells from cord blood	blood
2	chr6:37985000-38030200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:37985200-38001400	Weak transcription	Small Intestine	intestine
4	chr6:37988000-38001400	Weak transcription	Stomach Mucosa	stomach
5	chr6:37990600-38005800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr6:37993000-38001800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr6:37994400-38011400	Weak transcription	Aorta	Aorta
8	chr6:37995200-38000800	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr6:37995600-38001200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr6:37995800-38001200	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr6:37995800-38003800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr6:37995800-38005400	Weak transcription	Psoas Muscle	Psoas
13	chr6:37995800-38008000	Weak transcription	Fetal Muscle Leg	muscle
14	chr6:37995800-38013000	Weak transcription	Fetal Thymus	thymus
15	chr6:37995800-38020600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr6:37996000-38000800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr6:37996000-38001200	Weak transcription	Brain Substantia Nigra	brain
18	chr6:37996000-38001200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr6:37996000-38001200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr6:37996000-38001400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr6:37996000-38002000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr6:37996000-38002600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr6:37996000-38015400	Weak transcription	HSMMtube	muscle
24	chr6:37996200-38005400	Weak transcription	Brain Cingulate Gyrus	brain
25	chr6:37996200-38008000	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr6:37996200-38008600	Weak transcription	HUVEC	blood vessel
27	chr6:37996400-38001400	Weak transcription	Primary T cells from cord blood	blood
28	chr6:37996600-38001200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr6:37996600-38002000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr6:37996600-38002000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr6:37996600-38002400	Weak transcription	NHDF-Ad	bronchial
32	chr6:37997000-38001800	Weak transcription	Adipose Nuclei	Adipose
33	chr6:37997000-38002400	Weak transcription	Primary hematopoietic stem cells	blood
34	chr6:37997200-38001200	Weak transcription	Liver	Liver
35	chr6:37997200-38001800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr6:37997200-38002400	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr6:37997200-38002800	Weak transcription	Osteobl	bone
38	chr6:37997600-38002400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr6:37997600-38007000	Weak transcription	A549	lung
40	chr6:37997800-38002000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr6:37998400-38001000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr6:37998600-38029200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr6:37999200-38001000	Weak transcription	GM12878-XiMat	blood
44	chr6:37999200-38001600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr6:37999200-38001800	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr6:37999400-38002800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr6:37999400-38004800	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr6:37999400-38005000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr6:37999600-38001400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr6:37999800-38008400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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