Variant report

Variant	rs6042169
Chromosome Location	chr20:13473863-13473864
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	chr20:13467756..13469452-chr20:13473202..13474865,2	MCF-7	breast:

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2295502	0.81[CHB][hapmap];1.00[YRI][hapmap]
rs3827701	1.00[ASW][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];1.00[YRI][hapmap]
rs3827704	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6042224	0.83[TSI][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	nsv1062049	chr20:13347580-13477455	Enhancers ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv544186	chr20:13347580-13477455	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1061303	chr20:13395546-13810990	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv585435	chr20:13410638-13582476	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv916202	chr20:13421724-14043615	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv1059817	chr20:13422602-13807968	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv458871	chr20:13447896-13573415	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv585436	chr20:13447896-13573415	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv1066810	chr20:13451869-14432454	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13395600-13477800	Weak transcription	Gastric	stomach
2	chr20:13462200-13477800	Weak transcription	Thymus	Thymus
3	chr20:13463400-13480200	Weak transcription	Brain Angular Gyrus	brain
4	chr20:13463800-13481200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr20:13463800-13505400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr20:13464000-13474800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr20:13464000-13475200	Weak transcription	Fetal Kidney	kidney
8	chr20:13464000-13479000	Weak transcription	Duodenum Mucosa	Duodenum
9	chr20:13464000-13493800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr20:13464200-13475800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr20:13464200-13477800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr20:13464200-13478000	Weak transcription	Primary B cells from peripheral blood	blood
13	chr20:13464200-13479200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr20:13464200-13480200	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr20:13464200-13483400	Weak transcription	Fetal Thymus	thymus
16	chr20:13464400-13474800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr20:13464400-13479400	Weak transcription	Primary B cells from cord blood	blood
18	chr20:13465400-13480000	Strong transcription	Dnd41	blood
19	chr20:13467800-13477800	Weak transcription	Primary T cells from cord blood	blood
20	chr20:13468000-13483600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr20:13468200-13477800	Weak transcription	Aorta	Aorta
22	chr20:13468200-13481200	Weak transcription	Liver	Liver
23	chr20:13468200-13483600	Weak transcription	Right Ventricle	heart
24	chr20:13469600-13476600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr20:13470200-13505800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr20:13471000-13481000	Weak transcription	HepG2	liver
27	chr20:13471200-13474400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr20:13471200-13474400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr20:13471200-13474400	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr20:13471200-13474800	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr20:13471400-13474400	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr20:13471400-13475400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr20:13471400-13475400	Enhancers	Hela-S3	cervix
34	chr20:13471600-13474400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr20:13471800-13480000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr20:13471800-13483400	Weak transcription	Fetal Intestine Small	intestine
37	chr20:13472000-13474000	Enhancers	HMEC	breast
38	chr20:13472000-13474200	Enhancers	H1 Cell Line	embryonic stem cell
39	chr20:13472000-13474600	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr20:13472400-13474200	Active TSS	HSMMtube	muscle
41	chr20:13472600-13474200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr20:13472800-13474000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr20:13473000-13474000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr20:13473000-13475200	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr20:13473000-13475400	Enhancers	NHEK	skin
46	chr20:13473000-13480600	Weak transcription	NHLF	lung
47	chr20:13473200-13474200	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr20:13473200-13474200	Enhancers	iPS-20b Cell Line	embryonic stem cell
49	chr20:13473200-13474400	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr20:13473200-13475800	Weak transcription	Fetal Lung	lung

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