Variant report

Variant	rs6688227
Chromosome Location	chr1:247010734-247010735
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:247005474..247007845-chr1:247009959..247011844,2	K562	blood:

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1110068	1.00[ASW][hapmap];0.91[GIH][hapmap];0.85[LWK][hapmap];0.93[AFR][1000 genomes]
rs1630829	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1691251	0.81[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1892117	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2800222	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2996549	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2996550	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5021094	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6685066	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7526386	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7528980	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7530860	1.00[ASW][hapmap];0.81[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9783081	0.81[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.89[TSI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv873421	chr1:246818634-247044692	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv2762192	chr1:246823857-247069232	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh 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	52 gene(s)	inside rSNPs	diseases
5	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription 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	52 gene(s)	inside rSNPs	diseases
6	nsv1011346	chr1:246868799-247133898	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	esv1810844	chr1:246988018-247054824	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv873424	chr1:246991094-247366380	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246989200-247011200	Weak transcription	Fetal Kidney	kidney
2	chr1:247000200-247020200	Weak transcription	Spleen	Spleen
3	chr1:247001400-247012000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:247001400-247016400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:247001400-247020000	Weak transcription	Brain Substantia Nigra	brain
6	chr1:247002000-247038200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:247002200-247031400	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr1:247002200-247033800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:247002200-247034200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:247002200-247082400	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr1:247002400-247081000	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr1:247002800-247032600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:247002800-247043200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr1:247003000-247011000	Strong transcription	Duodenum Smooth Muscle	Duodenum
15	chr1:247003000-247015200	Weak transcription	Fetal Heart	heart
16	chr1:247003000-247015200	Weak transcription	NHLF	lung
17	chr1:247003000-247018600	Weak transcription	Fetal Brain Male	brain
18	chr1:247003200-247012000	Weak transcription	Psoas Muscle	Psoas
19	chr1:247003200-247015200	Weak transcription	Esophagus	oesophagus
20	chr1:247003200-247020400	Weak transcription	Gastric	stomach
21	chr1:247003200-247029200	Strong transcription	Fetal Thymus	thymus
22	chr1:247003200-247042200	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr1:247003200-247042800	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr1:247003400-247010800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr1:247003400-247022600	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr1:247003400-247043000	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr1:247003400-247044600	Strong transcription	Dnd41	blood
28	chr1:247004000-247013600	Strong transcription	Sigmoid Colon	Sigmoid Colon
29	chr1:247004000-247022200	Strong transcription	Fetal Intestine Large	intestine
30	chr1:247004000-247040800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr1:247004000-247041200	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr1:247004000-247042800	Strong transcription	Primary T cells from cord blood	blood
33	chr1:247004000-247053600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:247004200-247011600	Weak transcription	Small Intestine	intestine
35	chr1:247004200-247013000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr1:247004200-247013000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr1:247004200-247013200	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr1:247004200-247013400	Strong transcription	HSMMtube	muscle
39	chr1:247004200-247018400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:247004200-247021200	Strong transcription	A549	lung
41	chr1:247004200-247025200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr1:247004200-247025400	Strong transcription	Fetal Muscle Trunk	muscle
43	chr1:247004200-247042400	Strong transcription	Primary B cells from peripheral blood	blood
44	chr1:247004200-247042800	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr1:247004200-247043000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr1:247004200-247044400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr1:247004200-247044400	Strong transcription	Liver	Liver
48	chr1:247004200-247083400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:247004400-247012600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
50	chr1:247004400-247013000	Strong transcription	Hela-S3	cervix

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