Variant report

Variant	rs6688898
Chromosome Location	chr1:175971669-175971670
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:175970211..175972835-chr1:176041192..176042901,2	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10218714	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10436856	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10494495	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10753112	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10753117	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10753118	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10798422	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10798425	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10798434	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10798442	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10798444	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10913116	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10913117	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10913120	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10913124	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10913128	0.81[EUR][1000 genomes]
rs10913131	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10913132	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11810706	0.84[ASN][1000 genomes]
rs12029090	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12033847	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12033976	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12040241	0.80[EUR][1000 genomes]
rs12404596	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12735810	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17351562	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34973462	0.84[ASN][1000 genomes]
rs35846379	0.81[EUR][1000 genomes]
rs4409605	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6693299	0.80[EUR][1000 genomes]
rs6703511	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7515914	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7534058	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7534948	0.85[AMR][1000 genomes];0.83[EUR][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	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:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175946000-175996000	Weak transcription	HMEC	breast
2	chr1:175953800-175999600	Weak transcription	Colonic Mucosa	Colon
3	chr1:175954000-175977800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:175954000-175978000	Weak transcription	Left Ventricle	heart
5	chr1:175954000-175987800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:175957000-175981200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr1:175957600-175977400	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr1:175957600-175977400	Weak transcription	HSMM	muscle
9	chr1:175957800-176022000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr1:175958000-175977200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:175958000-175977200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr1:175958000-175977400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:175958000-175987800	Weak transcription	Fetal Thymus	thymus
14	chr1:175958200-175978000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr1:175958600-175977400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:175958600-175977400	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr1:175958600-175977400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:175958600-175977400	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr1:175958800-175980600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:175959200-175977400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:175959400-175977400	Weak transcription	Dnd41	blood
22	chr1:175960000-175977400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:175961000-175977600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr1:175961200-175977600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:175962400-175977800	Weak transcription	Primary hematopoietic stem cells	blood
26	chr1:175962400-175977800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr1:175968400-175977800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr1:175970400-175977400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:175970600-175977800	Weak transcription	A549	lung
30	chr1:175971400-175977400	Weak transcription	Fetal Lung	lung
31	chr1:175971400-175981200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr1:175971600-175981200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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