Variant report

Variant	rs16841237
Chromosome Location	chr1:197172066-197172067
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr1:197171989-197172165	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:197112577..197117711-chr1:197168565..197172597,7	K562	blood:
2	chr1:197112577..197117470-chr1:197168821..197172597,7	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CFHR5-2	chr1:197170771-197172215	NONHSAT008616

Variant related genes	Relation type
ZBTB41	TF binding region
ENSG00000066279	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1034162	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10429911	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10494748	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10494749	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10494750	1.00[CHB][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10494751	0.82[ASW][hapmap];0.88[LWK][hapmap];0.82[MKK][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10732295	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10732296	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10801594	1.00[CHB][hapmap]
rs11800461	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11801772	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11803081	1.00[AMR][1000 genomes]
rs11808524	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11808883	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11809356	0.83[ASW][hapmap]
rs11809963	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11810041	0.85[AMR][1000 genomes]
rs11811295	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11811814	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1337165	1.00[AMR][1000 genomes]
rs1412631	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1415217	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1556763	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1571964	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16841212	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16841214	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16841219	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16841220	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MKK][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16841270	0.81[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1759013	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1794003	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4915378	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs59820773	1.00[ASN][1000 genomes]
rs61170532	1.00[AMR][1000 genomes]
rs61172533	1.00[ASN][1000 genomes]
rs6677082	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6700604	1.00[ASN][1000 genomes]
rs6702338	1.00[ASN][1000 genomes]
rs6702739	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6703400	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7520503	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7534439	1.00[JPT][hapmap]
rs7535048	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528460	chr1:196542567-197446702	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv873071	chr1:197079671-197187605	Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv873072	chr1:197079671-197221248	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv873073	chr1:197107074-197221248	Flanking Active TSS Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197171200-197172200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr1:197171400-197172400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr1:197171600-197172200	Enhancers	Primary hematopoietic stem cells	blood
4	chr1:197171600-197172200	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr1:197171600-197172200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr1:197171600-197172200	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr1:197171600-197172200	Enhancers	Brain Angular Gyrus	brain
8	chr1:197171600-197172200	Enhancers	Brain Substantia Nigra	brain
9	chr1:197171600-197172200	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr1:197171600-197172200	Enhancers	HepG2	liver
11	chr1:197171600-197172400	Enhancers	Hela-S3	cervix
12	chr1:197171600-197172600	Enhancers	Primary T cells from cord blood	blood
13	chr1:197171600-197172600	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr1:197171600-197172600	Enhancers	Brain Hippocampus Middle	brain
15	chr1:197171600-197175600	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr1:197171600-197181800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:197171600-197181800	Weak transcription	Ovary	ovary
18	chr1:197171800-197172200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:197171800-197172200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:197171800-197172200	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr1:197171800-197172200	Enhancers	Fetal Lung	lung
22	chr1:197171800-197172200	Enhancers	Psoas Muscle	Psoas
23	chr1:197171800-197172200	Enhancers	NHLF	lung
24	chr1:197171800-197172600	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr1:197171800-197179600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr1:197171800-197181400	Weak transcription	Fetal Heart	heart
27	chr1:197172000-197172200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:197172000-197172200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:197172000-197172200	Enhancers	Muscle Satellite Cultured Cells	--
30	chr1:197172000-197172200	Flanking Active TSS	NHDF-Ad	bronchial
31	chr1:197172000-197172400	Enhancers	Dnd41	blood
32	chr1:197172000-197176000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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