Variant report

Variant	rs2502841
Chromosome Location	chr1:176088186-176088187
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:176087488..176090030-chr1:176090768..176093080,2	K562	blood:

Extended variants
information (count: 123 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs10158829	0.82[CHB][hapmap]
rs10494496	0.82[CHB][hapmap]
rs10494499	0.91[CEU][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs10737316	1.00[CHB][hapmap]
rs10798427	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10798428	0.84[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10798431	1.00[CHB][hapmap]
rs10798432	0.85[CHB][hapmap]
rs10798446	0.84[YRI][hapmap]
rs10913135	0.83[YRI][hapmap]
rs10913137	0.84[YRI][hapmap]
rs10913143	0.84[YRI][hapmap]
rs10913144	0.80[YRI][hapmap]
rs10913150	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11576471	0.87[ASN][1000 genomes]
rs11806468	0.82[CHB][hapmap]
rs12038027	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12239888	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs12403794	0.88[EUR][1000 genomes]
rs1357337	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes]
rs1522637	1.00[CHB][hapmap]
rs16849522	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs16849645	0.82[ASN][1000 genomes]
rs16849735	1.00[JPT][hapmap]
rs17351808	0.91[CEU][hapmap];0.88[TSI][hapmap]
rs17351933	0.91[CEU][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs17352072	0.86[EUR][1000 genomes]
rs17354252	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs1770643	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1831447	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs2039231	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2039232	1.00[CHB][hapmap];0.81[CHD][hapmap];0.81[ASN][1000 genomes]
rs2481627	0.94[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];1.00[TSI][hapmap];0.84[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481634	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481635	0.93[EUR][1000 genomes]
rs2481639	0.81[ASN][1000 genomes]
rs2481641	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.88[MKK][hapmap];0.90[ASN][1000 genomes]
rs2481642	0.83[ASN][1000 genomes]
rs2481647	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2481651	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2481653	1.00[CHB][hapmap];0.82[CHD][hapmap]
rs2481657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2502822	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]
rs2502824	1.00[CHB][hapmap]
rs2502826	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]
rs2502830	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2502832	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2502834	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.88[MKK][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2502835	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2502836	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2502842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2502847	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2861629	1.00[CHB][hapmap]
rs2861630	0.91[CEU][hapmap];0.92[TSI][hapmap]
rs3845368	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs4129061	0.88[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4304533	1.00[CHB][hapmap];0.82[CHD][hapmap]
rs4307526	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4314844	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4460596	0.91[CEU][hapmap]
rs4543747	1.00[CHB][hapmap]
rs4603086	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4650934	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4652143	0.82[CHB][hapmap];1.00[CHD][hapmap]
rs4652148	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs4652152	0.82[CHB][hapmap]
rs471534	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs533403	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs553852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs559341	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs56367284	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs580978	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58325269	0.81[ASN][1000 genomes]
rs598177	0.81[ASN][1000 genomes]
rs599326	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs602933	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs60719126	0.91[EUR][1000 genomes]
rs611883	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61821007	0.91[EUR][1000 genomes]
rs61821009	0.91[EUR][1000 genomes]
rs61821028	0.88[EUR][1000 genomes]
rs61821029	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61822662	0.86[EUR][1000 genomes]
rs6425368	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6684747	0.83[AMR][1000 genomes]
rs6687043	0.88[ASW][hapmap];0.86[LWK][hapmap];0.85[MKK][hapmap]
rs6688211	1.00[CHB][hapmap]
rs6704509	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs704825	0.81[ASN][1000 genomes]
rs704827	0.94[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];0.92[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs704830	0.85[CHB][hapmap]
rs704831	0.85[CHB][hapmap]
rs704832	0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs74127185	0.87[EUR][1000 genomes]
rs7517351	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7517503	0.84[YRI][hapmap]
rs7521561	1.00[CHB][hapmap]
rs7522442	1.00[CHB][hapmap]
rs7524972	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7525001	1.00[JPT][hapmap]
rs7536464	1.00[CHB][hapmap]
rs7537435	0.82[AMR][1000 genomes]
rs7539247	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[LWK][hapmap];0.89[MKK][hapmap]
rs7543769	1.00[CHB][hapmap]
rs7545043	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7545639	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7546538	0.90[ASN][1000 genomes]
rs7552181	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes]
rs7553184	1.00[CHB][hapmap]
rs7554913	0.91[CEU][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs791744	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs791795	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs791800	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs791801	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.98[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs796933	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs9783047	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	nsv872565	chr1:176058782-176172795	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2502841	PIGC	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:176048800-176107000	Weak transcription	HepG2	liver
2	chr1:176054400-176131600	Weak transcription	NH-A	brain
3	chr1:176055000-176141600	Weak transcription	Hela-S3	cervix
4	chr1:176065600-176154800	Weak transcription	Aorta	Aorta
5	chr1:176069000-176090200	Weak transcription	Fetal Kidney	kidney
6	chr1:176069000-176116400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr1:176069000-176139200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:176069200-176123200	Weak transcription	Osteobl	bone
9	chr1:176069200-176126600	Weak transcription	HMEC	breast
10	chr1:176069200-176138800	Weak transcription	HUVEC	blood vessel
11	chr1:176069400-176121200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:176070400-176091600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr1:176070400-176097800	Weak transcription	A549	lung
14	chr1:176070400-176107400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr1:176070400-176126400	Weak transcription	Brain Anterior Caudate	brain
16	chr1:176070400-176151400	Weak transcription	Pancreas	Pancrea
17	chr1:176070800-176102200	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr1:176070800-176102600	Weak transcription	Brain Hippocampus Middle	brain
19	chr1:176070800-176110600	Weak transcription	Small Intestine	intestine
20	chr1:176071000-176091600	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr1:176071600-176088600	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr1:176071600-176117800	Weak transcription	Gastric	stomach
23	chr1:176072000-176140600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr1:176072400-176108600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr1:176072600-176107400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr1:176072800-176114600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr1:176072800-176114800	Weak transcription	NHDF-Ad	bronchial
28	chr1:176072800-176126600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr1:176076200-176088800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr1:176076200-176102000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:176076200-176126000	Weak transcription	Ovary	ovary
32	chr1:176076200-176127800	Weak transcription	Esophagus	oesophagus
33	chr1:176079800-176088400	Weak transcription	HSMMtube	muscle
34	chr1:176079800-176105400	Weak transcription	Colon Smooth Muscle	Colon
35	chr1:176080000-176103400	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr1:176081200-176114800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:176081400-176088400	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr1:176083000-176126000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr1:176083400-176091000	Weak transcription	Primary hematopoietic stem cells	blood
40	chr1:176083400-176094600	Weak transcription	Fetal Lung	lung
41	chr1:176083600-176088400	Weak transcription	Rectal Smooth Muscle	rectum
42	chr1:176083600-176091400	Weak transcription	K562	blood
43	chr1:176083600-176102600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:176083800-176106200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr1:176084200-176091400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr1:176084400-176094600	Weak transcription	Primary T cells from cord blood	blood
47	chr1:176084800-176089400	Weak transcription	Fetal Muscle Trunk	muscle
48	chr1:176084800-176095200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr1:176085000-176101200	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr1:176085400-176089000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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