Variant report

Variant	rs6684596
Chromosome Location	chr1:180313672-180313673
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	chr1:180312511..180315750-chr1:180317439..180321619,4	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10494526	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10913960	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10913962	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10913963	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10913964	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10913967	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10913975	0.94[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10913977	0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10914021	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs10914022	0.88[CHB][hapmap];0.94[CHD][hapmap];0.84[JPT][hapmap]
rs12022629	1.00[EUR][1000 genomes]
rs12037744	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12069143	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12089448	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12403226	1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12404700	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12407684	0.88[CHB][hapmap]
rs12409923	0.89[ASN][1000 genomes]
rs1341924	0.88[GIH][hapmap]
rs2025593	0.98[ASN][1000 genomes]
rs2877481	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs36088499	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3737584	0.88[GIH][hapmap]
rs4543756	0.88[GIH][hapmap]
rs6425646	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs6670950	0.83[CHB][hapmap]
rs878641	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs912766	1.00[CHB][hapmap];0.88[JPT][hapmap]

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	nsv1003739	chr1:180027760-180483292	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv535217	chr1:180027760-180483292	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv832004	chr1:180128502-180335540	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv527918	chr1:180279710-180443808	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1013716	chr1:180287338-180477072	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
6	nsv535221	chr1:180287338-180477072	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
7	esv2762200	chr1:180300936-180493841	ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
8	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180281000-180329400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:180309600-180345400	Weak transcription	Primary T cells from cord blood	blood
3	chr1:180310000-180348200	Weak transcription	Primary B cells from cord blood	blood
4	chr1:180310400-180315000	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr1:180310400-180317400	Weak transcription	HMEC	breast
6	chr1:180312600-180313800	Enhancers	Brain Anterior Caudate	brain
7	chr1:180312600-180314000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr1:180312600-180314000	Enhancers	Fetal Heart	heart
9	chr1:180312600-180315800	Enhancers	Dnd41	blood
10	chr1:180312800-180313800	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr1:180312800-180313800	Enhancers	Fetal Lung	lung
12	chr1:180312800-180313800	Enhancers	HSMM	muscle
13	chr1:180312800-180314000	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr1:180312800-180314000	Enhancers	Brain Hippocampus Middle	brain
15	chr1:180312800-180314200	Enhancers	Fetal Brain Male	brain
16	chr1:180312800-180314200	Enhancers	Fetal Brain Female	brain
17	chr1:180312800-180323200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr1:180313000-180313800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr1:180313000-180314000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:180313000-180314000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:180313000-180314400	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr1:180313200-180313800	Enhancers	NHEK	skin
23	chr1:180313200-180314000	Enhancers	Brain Angular Gyrus	brain
24	chr1:180313200-180314000	Enhancers	Brain Substantia Nigra	brain
25	chr1:180313400-180313800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:180313400-180314200	Enhancers	GM12878-XiMat	blood
27	chr1:180313400-180321800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:180313400-180329400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr1:180313400-180335200	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr1:180313600-180317400	Weak transcription	Psoas Muscle	Psoas
31	chr1:180313600-180323200	Weak transcription	Ovary	ovary

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