Variant report

Variant	rs2502826
Chromosome Location	chr1:176043797-176043798
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:176042309..176045520-chr1:176046203..176049197,3	K562	blood:

Extended variants
information (count: 119 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10158829	0.82[CHB][hapmap]
rs10436864	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10494496	0.82[CHB][hapmap]
rs10494499	0.91[CEU][hapmap];0.92[TSI][hapmap]
rs10737315	0.85[ASN][1000 genomes]
rs10737316	1.00[CHB][hapmap]
rs10798427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10798428	0.85[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10798431	1.00[CHB][hapmap]
rs10798432	0.85[CHB][hapmap];0.92[YRI][hapmap]
rs10913150	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11576471	0.97[ASN][1000 genomes]
rs11806468	0.82[CHB][hapmap]
rs12029090	0.84[YRI][hapmap]
rs12038027	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12239888	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs12404181	0.87[EUR][1000 genomes]
rs1357337	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1522637	1.00[CHB][hapmap]
rs16849522	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs17351808	0.91[CEU][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs17351933	0.91[CEU][hapmap];0.87[TSI][hapmap]
rs17354252	0.91[CEU][hapmap]
rs1770643	0.94[AMR][1000 genomes]
rs1831447	0.82[CHB][hapmap]
rs2039231	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[ASN][1000 genomes]
rs2039232	1.00[CHB][hapmap];0.81[CHD][hapmap]
rs2481627	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.81[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2481634	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2481635	0.82[EUR][1000 genomes]
rs2481641	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs2481642	0.93[ASN][1000 genomes]
rs2481647	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2481651	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481653	1.00[CHB][hapmap];0.82[CHD][hapmap];0.81[ASN][1000 genomes]
rs2481657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2502822	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2502824	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2502825	0.81[ASN][1000 genomes]
rs2502830	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2502832	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2502834	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[ASN][1000 genomes]
rs2502835	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[ASN][1000 genomes]
rs2502836	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2502841	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2502842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2502847	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2861629	1.00[CHB][hapmap]
rs2861630	0.91[CEU][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs3845368	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs4129061	0.82[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4304533	1.00[CHB][hapmap];0.82[CHD][hapmap]
rs4307526	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4314844	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4460596	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs4543747	1.00[CHB][hapmap]
rs4601543	0.91[EUR][1000 genomes]
rs4603086	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4650934	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4652143	0.82[CHB][hapmap];1.00[CHD][hapmap];0.82[ASN][1000 genomes]
rs4652148	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs4652152	0.82[CHB][hapmap]
rs471534	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs533403	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs553852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs559341	1.00[CHB][hapmap]
rs56367284	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs580978	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs599326	1.00[CHB][hapmap]
rs602933	1.00[CHB][hapmap]
rs60964243	0.84[EUR][1000 genomes]
rs61186664	0.91[EUR][1000 genomes]
rs611883	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61820953	0.84[EUR][1000 genomes]
rs61820960	0.86[EUR][1000 genomes]
rs61820965	0.91[EUR][1000 genomes]
rs61820968	0.91[EUR][1000 genomes]
rs61820999	0.86[EUR][1000 genomes]
rs61821029	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61822767	0.86[EUR][1000 genomes]
rs6425367	0.85[ASN][1000 genomes]
rs6425368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6661828	0.85[ASN][1000 genomes]
rs6684747	0.91[AMR][1000 genomes]
rs6687043	0.82[ASW][hapmap];0.96[YRI][hapmap];0.85[ASN][1000 genomes]
rs6688211	1.00[CHB][hapmap];0.96[YRI][hapmap];0.85[ASN][1000 genomes]
rs6704509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs704827	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.89[LWK][hapmap];0.90[MEX][hapmap];0.96[MKK][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs704830	0.85[CHB][hapmap]
rs704831	0.85[CHB][hapmap]
rs704832	0.92[CHD][hapmap];1.00[JPT][hapmap]
rs74127154	0.84[EUR][1000 genomes]
rs7517351	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7521561	1.00[CHB][hapmap]
rs7522442	1.00[CHB][hapmap]
rs7524972	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7536464	1.00[CHB][hapmap]
rs7537435	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7539247	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[YRI][hapmap]
rs7543769	1.00[CHB][hapmap]
rs7545043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7545639	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7546538	1.00[ASN][1000 genomes]
rs7552181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7553184	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs7554913	0.91[CEU][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs791744	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs791795	0.86[AMR][1000 genomes]
rs791800	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs791801	0.94[ASW][hapmap];0.91[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.80[LWK][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs796933	1.00[CHB][hapmap]
rs9783047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9792842	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	nsv872564	chr1:176027978-176102808	Enhancers Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv548246	chr1:176043797-176136273	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2502826	PIGC	cis	cerebellum	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175976800-176046000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr1:175978200-176050600	Weak transcription	Aorta	Aorta
3	chr1:175978400-176069000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr1:175979600-176045400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:175994200-176065200	Weak transcription	Psoas Muscle	Psoas
6	chr1:176006000-176045200	Weak transcription	GM12878-XiMat	blood
7	chr1:176006200-176049000	Weak transcription	HSMM	muscle
8	chr1:176007800-176066400	Weak transcription	Fetal Brain Male	brain
9	chr1:176010200-176048000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr1:176010400-176066000	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr1:176012200-176044800	Weak transcription	Fetal Stomach	stomach
12	chr1:176012200-176045200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr1:176012200-176045200	Weak transcription	Esophagus	oesophagus
14	chr1:176012200-176045200	Weak transcription	Fetal Lung	lung
15	chr1:176012400-176045400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr1:176012400-176045800	Weak transcription	Brain Hippocampus Middle	brain
17	chr1:176012400-176048200	Weak transcription	Ovary	ovary
18	chr1:176012400-176048200	Weak transcription	Thymus	Thymus
19	chr1:176012400-176062800	Weak transcription	Lung	lung
20	chr1:176012400-176065800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:176012800-176047000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr1:176013000-176045000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:176014400-176045200	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr1:176021600-176045000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:176028000-176045400	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr1:176028200-176045400	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr1:176028200-176048200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr1:176028200-176079200	Weak transcription	HSMMtube	muscle
29	chr1:176028400-176047200	Weak transcription	A549	lung
30	chr1:176028400-176047800	Weak transcription	Hela-S3	cervix
31	chr1:176028400-176049600	Weak transcription	K562	blood
32	chr1:176028800-176047200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr1:176029600-176048000	Weak transcription	HepG2	liver
34	chr1:176030000-176047400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr1:176030600-176045600	Weak transcription	Primary hematopoietic stem cells	blood
36	chr1:176030800-176048200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:176031000-176054000	Weak transcription	NH-A	brain
38	chr1:176032000-176048200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr1:176034600-176045200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr1:176035000-176069800	Weak transcription	NHEK	skin
41	chr1:176035200-176067600	Weak transcription	Colonic Mucosa	Colon
42	chr1:176035400-176066400	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr1:176035400-176067200	Weak transcription	HUVEC	blood vessel
44	chr1:176035600-176046800	Weak transcription	Fetal Thymus	thymus
45	chr1:176036000-176053800	Weak transcription	Placenta	Placenta
46	chr1:176036400-176045200	Weak transcription	Colon Smooth Muscle	Colon
47	chr1:176036600-176049000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr1:176036800-176045800	Weak transcription	Fetal Muscle Trunk	muscle
49	chr1:176037000-176045600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr1:176037000-176048000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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