Variant report

Variant	rs9404029
Chromosome Location	chr6:101207184-101207185
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs13437380	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2055162	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2132170	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3949519	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4839791	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58406648	0.92[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs72610820	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72610821	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72610822	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7741500	0.87[EUR][1000 genomes]
rs7760406	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs846802	0.92[ASN][1000 genomes]
rs9322111	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9322116	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9322175	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9322222	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9377084	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs9377140	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9377231	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9377233	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9386226	1.00[EUR][1000 genomes]
rs9386229	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9386254	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9390513	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9390581	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9390671	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9399637	1.00[EUR][1000 genomes]
rs9399638	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9399654	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9399657	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9399668	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9404041	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9485236	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9485306	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9498017	1.00[EUR][1000 genomes]
rs9498063	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9498203	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9498392	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9498397	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949535	chr6:100740293-101469052	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv886445	chr6:101004751-101240763	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv886456	chr6:101049108-101277926	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1020692	chr6:101136992-101426071	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv604275	chr6:101158950-101277926	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv886457	chr6:101158950-101487473	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv1016353	chr6:101172705-101304041	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv1020400	chr6:101172705-101981665	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer 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
9	nsv538390	chr6:101172705-101981665	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv1024526	chr6:101192726-101241291	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:101166200-101211000	Weak transcription	NH-A	brain
2	chr6:101168600-101211200	Weak transcription	Osteobl	bone
3	chr6:101169000-101211000	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr6:101172800-101210800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr6:101173000-101209000	Weak transcription	K562	blood
6	chr6:101173000-101211000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr6:101175800-101211200	Weak transcription	Psoas Muscle	Psoas
8	chr6:101177000-101211600	Weak transcription	NHDF-Ad	bronchial
9	chr6:101182200-101214400	Weak transcription	A549	lung
10	chr6:101184400-101304600	Weak transcription	Hela-S3	cervix
11	chr6:101185400-101212600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr6:101186600-101208400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr6:101188400-101211400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr6:101189200-101209200	Weak transcription	Right Ventricle	heart
15	chr6:101190200-101211200	Weak transcription	Fetal Lung	lung
16	chr6:101190200-101211600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr6:101190600-101212600	Weak transcription	HSMMtube	muscle
18	chr6:101190800-101211000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr6:101190800-101216200	Weak transcription	Stomach Mucosa	stomach
20	chr6:101190800-101217400	Weak transcription	NHLF	lung
21	chr6:101191000-101208200	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr6:101191000-101209000	Weak transcription	Lung	lung
23	chr6:101191000-101211200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr6:101191000-101211400	Weak transcription	Fetal Thymus	thymus
25	chr6:101191200-101207200	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr6:101191200-101207200	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr6:101191200-101207800	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr6:101191200-101208200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr6:101191200-101209200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr6:101191200-101209200	Weak transcription	Fetal Stomach	stomach
31	chr6:101191200-101209800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr6:101191200-101211200	Weak transcription	Fetal Muscle Leg	muscle
33	chr6:101191200-101211400	Weak transcription	Adipose Nuclei	Adipose
34	chr6:101191200-101211600	Weak transcription	Fetal Muscle Trunk	muscle
35	chr6:101191200-101211600	Weak transcription	HepG2	liver
36	chr6:101191200-101211800	Weak transcription	Placenta	Placenta
37	chr6:101191400-101207800	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr6:101191400-101207800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr6:101191400-101207800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr6:101191400-101208200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr6:101191400-101208200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr6:101191400-101208600	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr6:101191400-101209000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr6:101191400-101209000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr6:101191400-101209000	Weak transcription	Aorta	Aorta
46	chr6:101191400-101209000	Weak transcription	Ovary	ovary
47	chr6:101191400-101209200	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr6:101191400-101211200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr6:101191400-101211200	Weak transcription	Primary hematopoietic stem cells	blood
50	chr6:101191400-101211400	Weak transcription	Rectal Mucosa Donor 31	rectum

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