Variant report

Variant	rs2502822
Chromosome Location	chr1:176036351-176036352
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	chr1:176035605..176038562-chr1:176039929..176042827,2	K562	blood:

Extended variants
information (count: 118 )
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];0.82[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	0.84[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];0.83[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	0.82[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];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2481651	0.97[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];0.92[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]
rs2502826	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]
rs2502830	0.84[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];0.83[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	0.81[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	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4314844	0.89[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	0.81[AFR][1000 genomes];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];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6661828	0.85[ASN][1000 genomes]
rs6684747	0.91[AMR][1000 genomes]
rs6687043	0.81[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];0.87[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	0.81[AFR][1000 genomes];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];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7545639	0.86[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];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9792842	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2502822	PIGC	cis	cerebellum	SCAN

Chromatin state (count:82 , 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	chr1:175989800-176036400	Weak transcription	Pancreas	Pancrea
6	chr1:175994200-176065200	Weak transcription	Psoas Muscle	Psoas
7	chr1:176004000-176036400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:176004200-176039800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:176006000-176045200	Weak transcription	GM12878-XiMat	blood
10	chr1:176006200-176049000	Weak transcription	HSMM	muscle
11	chr1:176007800-176066400	Weak transcription	Fetal Brain Male	brain
12	chr1:176010200-176048000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr1:176010400-176066000	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr1:176012200-176044800	Weak transcription	Fetal Stomach	stomach
15	chr1:176012200-176045200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr1:176012200-176045200	Weak transcription	Esophagus	oesophagus
17	chr1:176012200-176045200	Weak transcription	Fetal Lung	lung
18	chr1:176012400-176036400	Weak transcription	Fetal Muscle Leg	muscle
19	chr1:176012400-176036400	Weak transcription	Gastric	stomach
20	chr1:176012400-176036400	Weak transcription	Left Ventricle	heart
21	chr1:176012400-176036400	Weak transcription	Spleen	Spleen
22	chr1:176012400-176045400	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr1:176012400-176045800	Weak transcription	Brain Hippocampus Middle	brain
24	chr1:176012400-176048200	Weak transcription	Ovary	ovary
25	chr1:176012400-176048200	Weak transcription	Thymus	Thymus
26	chr1:176012400-176062800	Weak transcription	Lung	lung
27	chr1:176012400-176065800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr1:176012800-176036800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr1:176012800-176038000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr1:176012800-176040000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:176012800-176042600	Weak transcription	Liver	Liver
32	chr1:176012800-176047000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr1:176013000-176040000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr1:176013000-176045000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr1:176013400-176040000	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr1:176013600-176037600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr1:176013600-176040000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:176014400-176039800	Weak transcription	Primary B cells from peripheral blood	blood
39	chr1:176014400-176045200	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr1:176015400-176038000	Weak transcription	Dnd41	blood
41	chr1:176015400-176039000	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr1:176015400-176040200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr1:176015600-176040000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:176017000-176036400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr1:176017200-176036400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr1:176020800-176037600	Weak transcription	Adipose Nuclei	Adipose
47	chr1:176021600-176045000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr1:176022800-176039800	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr1:176024400-176036400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr1:176024400-176039800	Weak transcription	Primary B cells from cord blood	blood

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