Variant report

Variant	rs6684747
Chromosome Location	chr1:175969772-175969773
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10436864	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs10494495	0.80[YRI][hapmap]
rs10494499	0.81[CEU][hapmap]
rs10737316	0.85[CHB][hapmap]
rs10798427	0.91[CEU][hapmap];0.85[CHB][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10798428	0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10798431	0.85[CHB][hapmap]
rs10798432	0.90[YRI][hapmap]
rs10913109	0.81[AMR][1000 genomes]
rs10913150	0.86[AMR][1000 genomes]
rs12029090	0.89[YRI][hapmap]
rs12038027	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1357337	0.91[CEU][hapmap];0.85[CHB][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs1522637	0.85[CHB][hapmap]
rs17351808	0.81[CEU][hapmap]
rs17351933	0.81[CEU][hapmap]
rs17354252	0.81[CEU][hapmap]
rs1770643	0.86[AMR][1000 genomes]
rs2039231	0.85[CHB][hapmap];0.86[YRI][hapmap]
rs2039232	0.85[CHB][hapmap]
rs2481627	0.91[CEU][hapmap];0.85[CHB][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes]
rs2481634	0.86[AMR][1000 genomes]
rs2481641	0.85[CHB][hapmap];0.96[YRI][hapmap]
rs2481647	0.83[CEU][hapmap];0.85[CHB][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes]
rs2481651	0.91[AMR][1000 genomes]
rs2481653	0.85[CHB][hapmap]
rs2481657	0.91[CEU][hapmap];0.85[CHB][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes]
rs2502822	0.91[CEU][hapmap];0.85[CHB][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes]
rs2502824	0.85[CHB][hapmap]
rs2502826	0.91[CEU][hapmap];0.85[CHB][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes]
rs2502830	0.88[AMR][1000 genomes]
rs2502832	0.91[CEU][hapmap];0.85[CHB][hapmap];0.96[YRI][hapmap];0.88[AMR][1000 genomes]
rs2502834	0.85[CHB][hapmap];0.81[YRI][hapmap]
rs2502835	0.85[CHB][hapmap];0.83[YRI][hapmap]
rs2502836	0.91[CEU][hapmap];0.85[CHB][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes]
rs2502841	0.91[CEU][hapmap];0.85[CHB][hapmap];0.83[AMR][1000 genomes]
rs2502842	0.91[CEU][hapmap];0.85[CHB][hapmap];0.88[YRI][hapmap];0.86[AMR][1000 genomes]
rs2502847	0.86[AMR][1000 genomes]
rs2861629	0.85[CHB][hapmap]
rs2861630	0.81[CEU][hapmap]
rs4129061	0.90[CEU][hapmap];0.91[AMR][1000 genomes]
rs4304533	0.85[CHB][hapmap]
rs4307526	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs4314844	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs4409605	0.80[YRI][hapmap]
rs4460596	0.81[CEU][hapmap]
rs4543747	0.85[CHB][hapmap]
rs4603086	0.86[AMR][1000 genomes]
rs4650934	0.80[AMR][1000 genomes]
rs471534	0.86[AMR][1000 genomes]
rs553852	0.91[CEU][hapmap];0.85[CHB][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes]
rs559341	0.85[CHB][hapmap]
rs56367284	0.86[AMR][1000 genomes]
rs580978	0.86[AMR][1000 genomes]
rs599326	0.85[CHB][hapmap]
rs602933	0.85[CHB][hapmap]
rs611883	0.86[AMR][1000 genomes]
rs61821029	0.86[AMR][1000 genomes]
rs6425368	0.91[CEU][hapmap];0.85[CHB][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6678628	0.80[YRI][hapmap]
rs6687043	0.92[YRI][hapmap]
rs6688211	0.85[CHB][hapmap];0.93[YRI][hapmap]
rs6704509	0.91[CEU][hapmap];0.85[CHB][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs704827	0.91[CEU][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes]
rs7517351	0.91[CEU][hapmap];0.85[CHB][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7521561	1.00[CHB][hapmap]
rs7522442	0.85[CHB][hapmap]
rs7524972	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7536464	0.85[CHB][hapmap]
rs7537435	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs7539247	0.85[CHB][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs7543769	0.85[CHB][hapmap]
rs7545043	0.91[CEU][hapmap];0.85[CHB][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs7545639	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs7552181	0.91[CEU][hapmap];0.85[CHB][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs7553184	0.85[CHB][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs7554913	0.81[CEU][hapmap]
rs791744	0.91[CEU][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes]
rs791800	0.86[AMR][1000 genomes]
rs791801	0.83[CEU][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes]
rs796933	0.85[CHB][hapmap]
rs9783047	0.91[CEU][hapmap];0.85[CHB][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[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:31 , 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	chr1:175957800-175971200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr1:175957800-176022000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr1:175958000-175977200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:175958000-175977200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr1:175958000-175977400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:175958000-175987800	Weak transcription	Fetal Thymus	thymus
15	chr1:175958200-175978000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr1:175958600-175977400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:175958600-175977400	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr1:175958600-175977400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:175958600-175977400	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr1:175958800-175980600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:175959200-175977400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:175959400-175977400	Weak transcription	Dnd41	blood
23	chr1:175960000-175977400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:175961000-175971600	Weak transcription	Primary B cells from cord blood	blood
25	chr1:175961000-175977600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:175961200-175977600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:175962400-175977800	Weak transcription	Primary hematopoietic stem cells	blood
28	chr1:175962400-175977800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr1:175968400-175977800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr1:175968800-175971000	Weak transcription	Fetal Lung	lung
31	chr1:175969600-175969800	Enhancers	A549	lung

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