Variant report

Variant	rs2842501
Chromosome Location	chr6:38005878-38005879
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38005433..38007087-chr6:38019483..38021384,2	MCF-7	breast:
2	chr6:38004599..38007314-chr6:38011024..38013903,2	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11963886	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1496579	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890244	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890367	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2495213	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2645103	1.00[ASN][1000 genomes]
rs2645129	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2645133	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2645135	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2645136	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2645138	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2749920	1.00[ASN][1000 genomes]
rs2842502	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2842504	1.00[ASN][1000 genomes]
rs2842509	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2842518	1.00[ASN][1000 genomes]
rs2842519	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458033	1.00[ASN][1000 genomes]
rs6930917	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7765420	1.00[ASN][1000 genomes]
rs7775465	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9380711	1.00[ASN][1000 genomes]

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	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
9	nsv970298	chr6:38003938-38014330	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37985000-38030200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:37994400-38011400	Weak transcription	Aorta	Aorta
3	chr6:37995800-38008000	Weak transcription	Fetal Muscle Leg	muscle
4	chr6:37995800-38013000	Weak transcription	Fetal Thymus	thymus
5	chr6:37995800-38020600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr6:37996000-38015400	Weak transcription	HSMMtube	muscle
7	chr6:37996200-38008000	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr6:37996200-38008600	Weak transcription	HUVEC	blood vessel
9	chr6:37997600-38007000	Weak transcription	A549	lung
10	chr6:37998600-38029200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr6:37999800-38008400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr6:37999800-38017600	Weak transcription	Right Atrium	heart
13	chr6:37999800-38018600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr6:38001000-38028600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr6:38002400-38029400	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr6:38002600-38006600	Weak transcription	NHLF	lung
17	chr6:38002600-38008600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr6:38002800-38017800	Weak transcription	HSMM	muscle
19	chr6:38002800-38024400	Weak transcription	Fetal Stomach	stomach
20	chr6:38003000-38008400	Weak transcription	Fetal Lung	lung
21	chr6:38003000-38008600	Weak transcription	Brain Anterior Caudate	brain
22	chr6:38003000-38024800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr6:38003000-38025000	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr6:38003200-38024400	Weak transcription	Primary T cells from cord blood	blood
25	chr6:38003400-38007000	Weak transcription	Osteobl	bone
26	chr6:38003600-38006800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr6:38003600-38025400	Weak transcription	NHDF-Ad	bronchial
28	chr6:38003800-38008400	Weak transcription	Liver	Liver
29	chr6:38003800-38017800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:38004000-38008800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr6:38004000-38011000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr6:38004000-38018000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr6:38004000-38018200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr6:38004200-38007200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr6:38004200-38007200	Weak transcription	HepG2	liver
36	chr6:38004200-38008400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr6:38004200-38013600	Weak transcription	Small Intestine	intestine
38	chr6:38004200-38024600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr6:38004200-38029200	Weak transcription	Primary B cells from cord blood	blood
40	chr6:38005000-38006000	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr6:38005000-38006200	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr6:38005000-38006200	Enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr6:38005000-38006600	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr6:38005200-38006600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr6:38005400-38006000	Enhancers	Gastric	stomach
46	chr6:38005400-38006000	Enhancers	Left Ventricle	heart
47	chr6:38005400-38006000	Enhancers	Psoas Muscle	Psoas
48	chr6:38005400-38006200	Enhancers	Brain Cingulate Gyrus	brain
49	chr6:38005800-38006000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr6:38005800-38006000	Enhancers	Stomach Smooth Muscle	stomach

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