Variant report

Variant	rs6042669
Chromosome Location	chr20:14303777-14303778
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1040826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs17263597	0.82[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]
rs1998238	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap]
rs2038505	0.91[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs204605	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs204606	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs204608	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs204617	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap]
rs204625	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs204632	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs204633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs204638	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs204639	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs204643	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2208453	0.82[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2208455	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2256118	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2327840	0.81[EUR][1000 genomes]
rs2327841	0.86[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2327842	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2327843	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2327845	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2423778	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2423779	0.95[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2876376	0.80[ASN][1000 genomes]
rs370158	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs382674	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4384860	0.88[ASN][1000 genomes]
rs4814293	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs485293	0.87[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap]
rs58243986	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs58694064	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6033926	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap]
rs6033927	0.86[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6033931	0.86[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6033932	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6033933	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6033941	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6042629	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap]
rs6042630	0.94[JPT][hapmap]
rs6042642	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs6042648	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6042652	0.85[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6042653	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6074719	0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs6074720	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6074721	0.88[ASN][1000 genomes]
rs6074722	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6079355	0.82[CHB][hapmap]
rs6079380	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6135113	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs615331	0.86[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]
rs717327	0.95[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs718705	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7263144	0.87[CEU][hapmap]
rs7271710	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8116353	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8123052	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs982553	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs982554	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs994567	0.86[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[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	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
2	nsv531479	chr20:13632491-14434432	Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1057486	chr20:14077828-14469129	ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1066235	chr20:14173771-14389050	Weak transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv458872	chr20:14189779-14317390	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv470540	chr20:14189779-14317390	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv585439	chr20:14189779-14317390	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1055499	chr20:14224873-14848061	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv432101	chr20:14294196-14353346	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:14289600-14306400	Weak transcription	Fetal Intestine Small	intestine
2	chr20:14293000-14306200	Weak transcription	Colon Smooth Muscle	Colon
3	chr20:14294800-14304600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr20:14294800-14306400	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr20:14294800-14314000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr20:14295000-14305000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr20:14295000-14306000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr20:14296000-14312000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr20:14299000-14306200	Weak transcription	Fetal Lung	lung
10	chr20:14299200-14306400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr20:14300600-14305400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr20:14301800-14306400	Weak transcription	Fetal Intestine Large	intestine
13	chr20:14302200-14305200	Enhancers	NHEK	skin
14	chr20:14302400-14303800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr20:14302400-14304000	Weak transcription	Duodenum Mucosa	Duodenum
16	chr20:14302400-14304200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr20:14303600-14304000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr20:14303600-14304400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr20:14303600-14306000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr20:14303600-14307000	Genic enhancers	HMEC	breast
21	chr20:14303600-14308200	Strong transcription	Fetal Kidney	kidney
22	chr20:14303600-14323400	Weak transcription	Small Intestine	intestine

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