Variant report

Variant	rs6425369
Chromosome Location	chr1:175953329-175953330
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10798430	1.00[CHB][hapmap];0.81[YRI][hapmap]
rs10798435	1.00[CHB][hapmap]
rs1357338	1.00[CHB][hapmap];0.84[YRI][hapmap]
rs2481629	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2481632	1.00[CHB][hapmap]
rs2481636	0.81[AFR][1000 genomes]
rs2481640	1.00[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2481648	1.00[CHB][hapmap]
rs2481652	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2502820	0.84[AFR][1000 genomes]
rs2502821	1.00[CHB][hapmap]
rs2502827	1.00[CHB][hapmap]
rs2502828	1.00[CHB][hapmap]
rs2502833	0.83[AFR][1000 genomes]
rs2502837	1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2774925	1.00[CHB][hapmap]
rs4233165	1.00[CHB][hapmap]
rs4344283	1.00[CHB][hapmap]
rs4347169	1.00[CHB][hapmap]
rs4379645	1.00[CHB][hapmap]
rs4460596	1.00[CHB][hapmap]
rs4534339	1.00[CHB][hapmap]
rs4652146	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs598855	1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs613965	1.00[CHB][hapmap]
rs6425372	1.00[CHB][hapmap]
rs6425374	1.00[CHB][hapmap]
rs646754	1.00[CHB][hapmap]
rs6674353	1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6704250	1.00[CHB][hapmap]
rs704828	1.00[CHB][hapmap]
rs7523048	1.00[CHB][hapmap]
rs7525112	1.00[CHB][hapmap]
rs7532122	1.00[CHB][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7541563	1.00[CHB][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7554913	1.00[CHB][hapmap]
rs791748	1.00[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs998631	1.00[CHB][hapmap]

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	esv1823794	chr1:175869554-176311778	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS 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	33 gene(s)	inside rSNPs	diseases
2	nsv872561	chr1:175949646-176092167	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv872562	chr1:175949646-176141866	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv872563	chr1:175949646-176184625	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175904200-175956200	Weak transcription	Psoas Muscle	Psoas
2	chr1:175906400-175962600	Weak transcription	NH-A	brain
3	chr1:175908000-175959400	Weak transcription	NHEK	skin
4	chr1:175940400-175953800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:175945800-175953400	Weak transcription	Aorta	Aorta
6	chr1:175946000-175996000	Weak transcription	HMEC	breast
7	chr1:175948200-175957400	Weak transcription	Brain Substantia Nigra	brain
8	chr1:175948200-175961400	Weak transcription	NHLF	lung
9	chr1:175948400-175953400	Weak transcription	Colon Smooth Muscle	Colon
10	chr1:175948600-175953400	Weak transcription	HUVEC	blood vessel
11	chr1:175949200-175953400	Strong transcription	Primary T cells from cord blood	blood
12	chr1:175949200-175958600	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr1:175949200-175958600	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr1:175949400-175957000	Weak transcription	Osteobl	bone
15	chr1:175949600-175954800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:175949800-175954800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:175950000-175954000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:175950000-175954200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:175950000-175961200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:175950200-175955400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:175950200-175956400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:175950400-175954800	ZNF genes & repeats	Primary B cells from cord blood	blood
23	chr1:175950400-175955000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
24	chr1:175950400-175955000	ZNF genes & repeats	GM12878-XiMat	blood
25	chr1:175950600-175953600	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr1:175950600-175954800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
27	chr1:175950800-175953800	ZNF genes & repeats	Liver	Liver
28	chr1:175951000-175953800	ZNF genes & repeats	Adipose Nuclei	Adipose
29	chr1:175951000-175954000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
30	chr1:175951000-175955000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr1:175951200-175953400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:175951200-175953400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:175951200-175953400	ZNF genes & repeats	Fetal Intestine Large	intestine
34	chr1:175951200-175953800	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr1:175951200-175957600	Strong transcription	HSMM	muscle
36	chr1:175951400-175954000	Strong transcription	Placenta Amnion	Placenta Amnion
37	chr1:175951400-175954200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
38	chr1:175951400-175954800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
39	chr1:175951600-175953600	Strong transcription	Dnd41	blood
40	chr1:175951600-175954600	Strong transcription	Muscle Satellite Cultured Cells	--
41	chr1:175951600-175956200	Strong transcription	Hela-S3	cervix
42	chr1:175951600-175958600	Weak transcription	Fetal Heart	heart
43	chr1:175951800-175953600	ZNF genes & repeats	Fetal Muscle Leg	muscle
44	chr1:175951800-175953800	ZNF genes & repeats	Brain Germinal Matrix	brain
45	chr1:175951800-175954000	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
46	chr1:175951800-175954200	ZNF genes & repeats	Primary B cells from peripheral blood	blood
47	chr1:175951800-175954600	ZNF genes & repeats	A549	lung
48	chr1:175951800-175954800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr1:175951800-175954800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr1:175951800-175954800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell

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