Variant report

Variant	rs6426323
Chromosome Location	chr1:246869974-246869975
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:246857655..246865600-chr1:246867157..246874213,9	MCF-7	breast:
2	chr1:246867425..246870263-chr1:246871598..246874190,3	MCF-7	breast:
3	chr1:246869676..246875291-chr1:246885182..246892205,11	MCF-7	breast:
4	chr1:246867885..246870245-chr1:246910384..246912809,2	MCF-7	breast:
5	chr1:246868796..246870534-chr1:246889935..246891767,2	K562	blood:
6	chr1:246867596..246871068-chr1:246871868..246876366,5	MCF-7	breast:
7	chr1:246866395..246870620-chr1:246886545..246889011,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143653	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10127783	0.87[CHB][hapmap]
rs10159002	0.87[CHB][hapmap]
rs10754532	0.87[CHB][hapmap];0.82[ASN][1000 genomes]
rs10924820	0.87[CHB][hapmap]
rs10924823	0.87[CHB][hapmap]
rs10924824	0.87[CHB][hapmap]
rs12085330	0.87[CHB][hapmap]
rs12122102	0.87[CHB][hapmap]
rs12132038	0.87[CHB][hapmap]
rs12725791	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3007307	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3007308	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3007309	0.86[EUR][1000 genomes]
rs3007310	0.90[EUR][1000 genomes]
rs3007311	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3007312	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3007313	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3007316	0.87[CHB][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs3007317	0.88[ASN][1000 genomes]
rs3007318	0.83[ASN][1000 genomes]
rs3007322	0.87[CHB][hapmap];0.83[ASN][1000 genomes]
rs3007323	0.81[ASN][1000 genomes]
rs3007324	0.81[CHB][hapmap];0.81[ASN][1000 genomes]
rs3007411	0.85[ASN][1000 genomes]
rs3795463	0.87[CHB][hapmap]
rs3795464	0.87[CHB][hapmap]
rs4244627	0.87[CHB][hapmap]
rs4926459	0.87[CHB][hapmap]
rs6426322	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6426326	0.87[CHB][hapmap];0.87[ASN][1000 genomes]
rs6664883	0.87[CHB][hapmap]
rs6685364	0.87[CHB][hapmap]
rs72764626	0.87[ASN][1000 genomes]
rs7364715	0.83[ASN][1000 genomes]
rs7416239	0.87[CHB][hapmap];0.87[ASN][1000 genomes]
rs7520737	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7526537	0.89[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7532928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7532929	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9426213	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9426218	0.81[CHB][hapmap]
rs9426269	0.82[ASN][1000 genomes]
rs9426271	0.80[CHB][hapmap];0.82[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	nsv1002805	chr1:246608164-246890518	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv535413	chr1:246608164-246890518	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	nsv430413	chr1:246845971-246975015	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer 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
9	nsv873422	chr1:246854862-247002638	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS 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
10	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

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246862600-246872800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:246862800-246871000	Weak transcription	Fetal Intestine Small	intestine
3	chr1:246863000-246871000	Weak transcription	Primary B cells from cord blood	blood
4	chr1:246866600-246874000	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr1:246867000-246870200	Enhancers	Placenta	Placenta
6	chr1:246867400-246871000	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr1:246867400-246872400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr1:246867400-246872600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr1:246867600-246870800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr1:246867800-246870200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr1:246867800-246870200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:246867800-246870800	Weak transcription	Dnd41	blood
13	chr1:246868000-246870000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr1:246868000-246870200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr1:246868000-246870400	Weak transcription	Stomach Mucosa	stomach
16	chr1:246868000-246870800	Weak transcription	Small Intestine	intestine
17	chr1:246868800-246870000	Enhancers	Hela-S3	cervix
18	chr1:246869000-246871000	Enhancers	Monocytes-CD14+_RO01746	blood
19	chr1:246869200-246870000	Weak transcription	Fetal Intestine Large	intestine
20	chr1:246869200-246870800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:246869200-246871200	Weak transcription	NHLF	lung
22	chr1:246869400-246870600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr1:246869400-246871000	Weak transcription	Osteobl	bone
24	chr1:246869600-246870000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:246869600-246870000	Enhancers	NHDF-Ad	bronchial
26	chr1:246869600-246870200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:246869800-246870000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:246869800-246870200	Enhancers	Placenta Amnion	Placenta Amnion
29	chr1:246869800-246872600	Enhancers	HepG2	liver
30	chr1:246869800-246873200	Enhancers	Liver	Liver

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