Variant report

Variant	rs4946562
Chromosome Location	chr6:121625056-121625057
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	chr6:121622881..121625518-chr6:121651420..121653237,2	MCF-7	breast:

Extended variants
information (count: 121 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs10428866	0.86[CHB][hapmap]
rs11154003	0.85[ASN][1000 genomes]
rs11154014	0.86[CEU][hapmap];0.88[EUR][1000 genomes]
rs12209087	0.85[EUR][1000 genomes]
rs1273715	0.85[CEU][hapmap]
rs1273718	0.92[CEU][hapmap]
rs1273720	1.00[CEU][hapmap]
rs1273721	0.84[CEU][hapmap]
rs1273722	0.84[CEU][hapmap]
rs1273725	0.91[CEU][hapmap]
rs1273726	0.91[CEU][hapmap]
rs1273728	0.85[CEU][hapmap]
rs1273732	1.00[CEU][hapmap]
rs1273733	0.85[CEU][hapmap]
rs1273738	1.00[CEU][hapmap]
rs1273742	1.00[CEU][hapmap]
rs1273745	0.84[CEU][hapmap]
rs1273746	0.85[CEU][hapmap]
rs1273748	0.85[CEU][hapmap]
rs1343072	0.85[ASN][1000 genomes]
rs1604279	0.85[ASN][1000 genomes]
rs17083165	0.83[CEU][hapmap]
rs17083190	0.85[CEU][hapmap]
rs1776810	0.86[CHB][hapmap]
rs1776817	0.84[CEU][hapmap]
rs1827299	0.85[ASN][1000 genomes]
rs1846865	0.80[EUR][1000 genomes]
rs1846866	0.85[CEU][hapmap]
rs1891646	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs1995313	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs2102102	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2133991	0.86[CHB][hapmap]
rs2133992	0.85[CEU][hapmap];0.93[CHB][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2455056	0.84[CEU][hapmap]
rs2797955	0.84[CEU][hapmap]
rs2892766	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2995680	0.84[CEU][hapmap]
rs35583988	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs407586	0.85[CEU][hapmap]
rs4395765	0.85[EUR][1000 genomes]
rs4412234	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs4412244	0.89[EUR][1000 genomes]
rs4461766	0.86[CEU][hapmap];0.90[EUR][1000 genomes]
rs4476866	0.85[CEU][hapmap];0.93[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs4610600	0.85[CHB][hapmap]
rs4946547	0.85[CEU][hapmap];0.93[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs4946563	0.86[CHB][hapmap]
rs4946565	0.82[EUR][1000 genomes]
rs6569180	0.86[CHB][hapmap]
rs6569197	0.88[EUR][1000 genomes]
rs6569200	0.82[EUR][1000 genomes]
rs6903298	0.84[EUR][1000 genomes]
rs6911380	0.84[EUR][1000 genomes]
rs6916050	0.86[EUR][1000 genomes]
rs6919890	0.88[EUR][1000 genomes]
rs6926502	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs6928060	0.87[EUR][1000 genomes]
rs6936507	0.88[ASN][1000 genomes]
rs7450022	0.85[CEU][hapmap];0.93[CHB][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7450632	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs7751291	1.00[CEU][hapmap]
rs7767455	0.85[CHB][hapmap]
rs7768058	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs785400	0.85[CHB][hapmap]
rs905024	0.85[CEU][hapmap];0.93[CHB][hapmap];0.83[JPT][hapmap];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs905025	0.85[CEU][hapmap];0.93[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs924528	0.83[ASN][1000 genomes]
rs9320793	0.82[CEU][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9320794	0.84[CEU][hapmap];0.92[CHB][hapmap];0.81[JPT][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9320802	0.85[CHB][hapmap]
rs9320806	0.85[EUR][1000 genomes]
rs9320807	0.85[EUR][1000 genomes]
rs9320808	0.83[EUR][1000 genomes]
rs9372640	0.85[CEU][hapmap];0.93[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs9372641	0.85[ASN][1000 genomes]
rs9372642	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9372643	0.85[ASN][1000 genomes]
rs9372644	0.85[ASN][1000 genomes]
rs9372646	0.85[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9372647	0.88[ASN][1000 genomes]
rs9375006	0.82[JPT][hapmap]
rs9375007	0.82[ASN][1000 genomes]
rs9375008	0.82[ASN][1000 genomes]
rs9375009	0.85[ASN][1000 genomes]
rs9375011	0.84[CEU][hapmap];0.92[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs9375012	0.85[CEU][hapmap];0.93[CHB][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9375022	0.86[CEU][hapmap];0.89[EUR][1000 genomes]
rs9385187	0.85[CEU][hapmap]
rs9385193	0.84[EUR][1000 genomes]
rs9387920	0.86[CEU][hapmap]
rs9387924	0.85[CEU][hapmap]
rs9387926	0.85[ASN][1000 genomes]
rs9387928	0.85[ASN][1000 genomes]
rs9387929	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs9387930	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9387939	0.90[EUR][1000 genomes]
rs9387942	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs9398622	0.85[CEU][hapmap]
rs9398623	0.84[CEU][hapmap];0.92[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9398625	0.85[CEU][hapmap];0.93[CHB][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9398631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9401373	0.85[ASN][1000 genomes]
rs9401374	0.85[CEU][hapmap];0.93[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs9401375	0.92[CEU][hapmap];0.92[CHB][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9401376	0.85[ASN][1000 genomes]
rs9401377	0.85[ASN][1000 genomes]
rs9401378	0.81[JPT][hapmap]
rs9401379	0.85[CEU][hapmap];0.93[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs9401380	0.86[EUR][1000 genomes]
rs9401382	0.85[EUR][1000 genomes]
rs9401387	0.83[EUR][1000 genomes]
rs9482119	0.86[CEU][hapmap]
rs9490136	0.85[CHB][hapmap]
rs9490149	0.85[CHB][hapmap]
rs953616	1.00[CEU][hapmap]
rs975679	0.84[CEU][hapmap]
rs976611	0.86[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023384	chr6:121235867-121683448	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv530527	chr6:121298528-121789855	ZNF genes & repeats Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv830789	chr6:121581450-121732320	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1017944	chr6:121600538-121644362	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:121586400-121655000	Weak transcription	Fetal Muscle Trunk	muscle
2	chr6:121588400-121655200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr6:121588800-121642000	Weak transcription	Left Ventricle	heart
4	chr6:121589000-121632800	Weak transcription	Fetal Lung	lung
5	chr6:121589000-121635200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr6:121589000-121637600	Weak transcription	Ovary	ovary
7	chr6:121589000-121654200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:121589200-121630000	Weak transcription	Fetal Intestine Large	intestine
9	chr6:121589200-121631800	Weak transcription	Fetal Intestine Small	intestine
10	chr6:121589200-121655000	Weak transcription	Fetal Stomach	stomach
11	chr6:121590200-121630800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:121594200-121654800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr6:121601600-121635200	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr6:121602600-121637800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:121603000-121632600	Weak transcription	Primary B cells from peripheral blood	blood
16	chr6:121604000-121645200	Weak transcription	Fetal Kidney	kidney
17	chr6:121604400-121642000	Weak transcription	Primary B cells from cord blood	blood
18	chr6:121604800-121653000	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr6:121606600-121655000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr6:121611000-121630800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr6:121611000-121640400	Weak transcription	Brain Cingulate Gyrus	brain
22	chr6:121611200-121655000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr6:121612600-121637600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr6:121613200-121637600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr6:121613400-121631000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr6:121613400-121640400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr6:121614000-121630600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr6:121614200-121631600	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr6:121614200-121633200	Weak transcription	Dnd41	blood
30	chr6:121614200-121640400	Weak transcription	Brain Hippocampus Middle	brain
31	chr6:121615600-121655000	Weak transcription	Pancreas	Pancrea
32	chr6:121616000-121630000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr6:121616200-121655000	Weak transcription	Fetal Muscle Leg	muscle
34	chr6:121617200-121651600	Weak transcription	GM12878-XiMat	blood
35	chr6:121617800-121628600	Weak transcription	Primary T cells from cord blood	blood
36	chr6:121619000-121640400	Weak transcription	Brain Anterior Caudate	brain
37	chr6:121619200-121630800	Weak transcription	Osteobl	bone
38	chr6:121620200-121640400	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr6:121622200-121654600	Weak transcription	Fetal Thymus	thymus
40	chr6:121622600-121655000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr6:121622800-121640400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr6:121622800-121654800	Weak transcription	Brain Germinal Matrix	brain
43	chr6:121623200-121626800	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr6:121623600-121630800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr6:121624200-121644800	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr6:121624600-121626000	Weak transcription	Pancreatic Islets	Pancreatic Islet

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