Variant report

Variant	rs2645124
Chromosome Location	chr6:37949615-37949616
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	chr6:37948324..37950868-chr6:37959290..37962178,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10485029	0.96[CEU][hapmap];0.86[CHB][hapmap];0.94[YRI][hapmap];0.82[EUR][1000 genomes]
rs1074234	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10947707	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10947713	0.83[CEU][hapmap];0.86[CHB][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes]
rs1187421	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.86[ASN][1000 genomes]
rs12190570	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12194275	0.80[CEU][hapmap]
rs12194618	0.86[CHB][hapmap]
rs12200258	0.86[CHB][hapmap]
rs12204352	0.85[CHB][hapmap]
rs12211248	0.86[CHB][hapmap]
rs12211981	0.86[CHB][hapmap]
rs12213835	0.86[CHB][hapmap]
rs13196716	0.80[CEU][hapmap]
rs13210701	0.86[CHB][hapmap]
rs16890344	0.86[CHB][hapmap]
rs171831	0.83[AFR][1000 genomes]
rs2055206	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2295791	0.80[CEU][hapmap]
rs259679	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs259686	0.86[CHB][hapmap]
rs259689	0.86[CHB][hapmap]
rs259690	0.86[CHB][hapmap]
rs259691	0.86[CHB][hapmap]
rs259695	0.85[AFR][1000 genomes]
rs259713	0.86[CHB][hapmap]
rs259718	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2645102	0.81[CEU][hapmap];0.86[CHB][hapmap]
rs2645107	0.81[CEU][hapmap];0.86[CHB][hapmap]
rs2645113	0.88[AFR][1000 genomes]
rs2645116	0.81[CEU][hapmap];0.86[CHB][hapmap]
rs2645117	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2645120	0.93[AFR][1000 genomes]
rs2645127	0.93[AFR][1000 genomes]
rs2645131	0.83[CEU][hapmap];0.84[CHB][hapmap]
rs2645134	0.80[CEU][hapmap];0.86[CHB][hapmap]
rs2645137	0.83[AFR][1000 genomes]
rs2842517	0.86[CHB][hapmap]
rs2842527	0.86[CHB][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes]
rs2842529	0.88[AFR][1000 genomes]
rs34592529	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35806631	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35925070	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56098839	0.90[AFR][1000 genomes]
rs6458041	0.80[CEU][hapmap]
rs7747130	0.80[CEU][hapmap];0.86[CHB][hapmap]

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	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	nsv1024016	chr6:37567651-37981590	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	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
4	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
5	nsv1018711	chr6:37813397-37981590	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	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
7	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
8	nsv602956	chr6:37909084-37986489	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	esv2761037	chr6:37930659-37966762	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37922800-37957600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:37922800-37958600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:37926800-37955000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:37929400-37953200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:37934400-37949800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr6:37942400-37953200	Weak transcription	Esophagus	oesophagus
7	chr6:37942800-37953600	Weak transcription	HepG2	liver
8	chr6:37942800-37956800	Weak transcription	Aorta	Aorta
9	chr6:37943000-37949800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr6:37943000-37951600	Weak transcription	NHDF-Ad	bronchial
11	chr6:37943000-37953000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr6:37943000-37955800	Weak transcription	Fetal Heart	heart
13	chr6:37943200-37951600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr6:37943600-37951800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr6:37943600-37952400	Weak transcription	Gastric	stomach
16	chr6:37944800-37952000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr6:37945800-37949800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr6:37946200-37950400	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr6:37946200-37953200	Weak transcription	GM12878-XiMat	blood
20	chr6:37946800-37950400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr6:37946800-37955800	Weak transcription	Primary B cells from cord blood	blood
22	chr6:37947000-37949800	Enhancers	Psoas Muscle	Psoas
23	chr6:37947000-37950400	Enhancers	Duodenum Mucosa	Duodenum
24	chr6:37947200-37949800	Enhancers	Brain Anterior Caudate	brain
25	chr6:37947200-37949800	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr6:37947200-37950000	Enhancers	Brain Hippocampus Middle	brain
27	chr6:37947200-37950000	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr6:37947200-37950200	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr6:37947200-37950400	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr6:37947200-37950400	Enhancers	Brain Substantia Nigra	brain
31	chr6:37947200-37950600	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr6:37947200-37951600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr6:37947400-37949800	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr6:37947400-37949800	Enhancers	Small Intestine	intestine
35	chr6:37947400-37950400	Enhancers	Brain Cingulate Gyrus	brain
36	chr6:37947400-37950400	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr6:37947400-37951800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr6:37947600-37949800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr6:37947800-37949800	Enhancers	Adipose Nuclei	Adipose
40	chr6:37947800-37949800	Enhancers	Brain Angular Gyrus	brain
41	chr6:37947800-37950400	Enhancers	Primary B cells from peripheral blood	blood
42	chr6:37948000-37952000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr6:37948000-37954400	Weak transcription	A549	lung
44	chr6:37948000-37955400	Weak transcription	Left Ventricle	heart
45	chr6:37948000-37955400	Weak transcription	Rectal Smooth Muscle	rectum
46	chr6:37948000-37956800	Weak transcription	Pancreas	Pancrea
47	chr6:37948200-37951400	Weak transcription	NHEK	skin
48	chr6:37948200-37955200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr6:37948200-37955600	Weak transcription	Primary hematopoietic stem cells	blood
50	chr6:37948400-37951200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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