Variant report

Variant	rs2780226
Chromosome Location	chr6:34199092-34199093
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:34198528..34202334-chr6:34358171..34361239,4	K562	blood:
2	chr6:34198585..34200548-chr6:34204064..34208861,4	MCF-7	breast:
3	chr6:34198109..34200070-chr6:34392390..34394637,3	MCF-7	breast:
4	chr6:34197271..34199519-chr6:34383050..34384850,2	K562	blood:

Variant related genes	Relation type
ENSG00000124614	Chromatin interaction
ENSG00000270800	Chromatin interaction
ENSG00000272325	Chromatin interaction
ENSG00000137309	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10807136	1.00[JPT][hapmap]
rs10807137	0.85[ASN][1000 genomes]
rs10807139	0.82[ASN][1000 genomes]
rs10947487	0.82[ASN][1000 genomes]
rs1150777	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1150779	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1150781	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1187115	0.87[ASN][1000 genomes]
rs1187118	0.87[ASN][1000 genomes]
rs11967909	0.83[JPT][hapmap]
rs1211163	0.87[ASN][1000 genomes]
rs12214804	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1573905	0.88[CHB][hapmap];0.95[CHD][hapmap]
rs1592269	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1759627	0.99[ASN][1000 genomes]
rs1759628	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1759645	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1759646	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1776877	0.88[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs1776897	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1776898	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1776899	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2797963	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2797964	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4711385	1.00[JPT][hapmap]
rs4713765	0.86[CHB][hapmap]
rs4713766	1.00[JPT][hapmap]
rs56348792	0.80[ASN][1000 genomes]
rs6457769	0.88[CHB][hapmap]
rs6909732	0.88[CHB][hapmap];0.95[CHD][hapmap]
rs6918981	0.90[CHD][hapmap]
rs7742369	0.88[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7749848	0.84[ASN][1000 genomes]
rs7751671	0.81[ASN][1000 genomes]
rs7774122	0.84[ASN][1000 genomes]
rs9357174	0.87[ASN][1000 genomes]
rs9366846	1.00[CHB][hapmap];0.95[CHD][hapmap]
rs9394200	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[MEX][hapmap]
rs9469745	0.87[AMR][1000 genomes]
rs9469761	0.88[CHB][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	nsv432881	chr6:34026522-34213822	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv885781	chr6:34110257-34247661	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv462903	chr6:34110257-34263743	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv602863	chr6:34110257-34263743	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	esv1816380	chr6:34110880-34206718	Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
6	nsv885782	chr6:34187206-34209516	Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
7	nsv885783	chr6:34187206-34209844	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv885784	chr6:34187206-34246714	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Height	20881960	GWAS catalog

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34192400-34199800	Weak transcription	Gastric	stomach
2	chr6:34192400-34200600	Weak transcription	HSMM	muscle
3	chr6:34192400-34202600	Weak transcription	Right Atrium	heart
4	chr6:34192400-34203400	Weak transcription	Pancreas	Pancrea
5	chr6:34192400-34203600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr6:34192600-34203600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr6:34192600-34204400	Weak transcription	HSMMtube	muscle
8	chr6:34192800-34203800	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr6:34194400-34203400	Weak transcription	Stomach Mucosa	stomach
10	chr6:34194800-34203600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr6:34195600-34199200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr6:34195600-34200800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr6:34195800-34200000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:34195800-34201000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr6:34195800-34201400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr6:34195800-34202400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:34195800-34203400	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr6:34195800-34203400	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr6:34195800-34203400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr6:34195800-34203400	Weak transcription	A549	lung
21	chr6:34195800-34203600	Weak transcription	Spleen	Spleen
22	chr6:34196000-34200600	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr6:34196000-34200600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr6:34196000-34200800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr6:34196000-34200800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr6:34196000-34202600	Weak transcription	Thymus	Thymus
27	chr6:34196200-34200400	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr6:34196200-34200800	Enhancers	Placenta	Placenta
29	chr6:34196400-34202600	Weak transcription	Primary B cells from cord blood	blood
30	chr6:34196600-34199200	Enhancers	NHEK	skin
31	chr6:34196600-34202400	Weak transcription	Primary hematopoietic stem cells	blood
32	chr6:34197000-34202800	Weak transcription	Primary B cells from peripheral blood	blood
33	chr6:34197200-34199800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr6:34197200-34203400	Weak transcription	Fetal Muscle Leg	muscle
35	chr6:34197400-34200600	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr6:34197400-34200600	Weak transcription	NHDF-Ad	bronchial
37	chr6:34197400-34200600	Weak transcription	Osteobl	bone
38	chr6:34197400-34201400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr6:34197400-34202400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr6:34197400-34202600	Weak transcription	Fetal Thymus	thymus
41	chr6:34197400-34203400	Weak transcription	K562	blood
42	chr6:34197400-34203600	Weak transcription	NHLF	lung
43	chr6:34198000-34203400	Weak transcription	GM12878-XiMat	blood
44	chr6:34198200-34199200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr6:34198200-34200600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr6:34198200-34203400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr6:34198400-34199200	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr6:34198400-34199400	Enhancers	Monocytes-CD14+_RO01746	blood
49	chr6:34198400-34202400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr6:34198400-34203200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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