Variant report

Variant	rs4424469
Chromosome Location	chr1:180393330-180393331
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:180380729..180383084-chr1:180391274..180393848,2	K562	blood:
2	chr1:180384412..180386137-chr1:180393141..180396163,3	K562	blood:
3	chr1:180391869..180395184-chr1:180397658..180400952,4	K562	blood:

Variant related genes	Relation type
ENSG00000135847	Chromatin interaction

Extended variants
information (count: 134 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs10158367	0.81[ASN][1000 genomes]
rs10494527	0.83[ASN][1000 genomes]
rs10737342	0.88[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753209	0.81[CHB][hapmap];0.83[ASN][1000 genomes]
rs10753211	0.82[ASN][1000 genomes]
rs10753212	0.82[ASN][1000 genomes]
rs10798745	0.83[CHB][hapmap];0.84[ASN][1000 genomes]
rs10798752	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798753	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798754	1.00[ASN][1000 genomes]
rs10798756	0.83[ASN][1000 genomes]
rs10798757	0.83[ASN][1000 genomes]
rs10798759	0.83[ASN][1000 genomes]
rs10798760	0.82[ASN][1000 genomes]
rs10798761	0.88[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798762	0.81[ASN][1000 genomes]
rs10798766	0.82[ASN][1000 genomes]
rs10798767	0.89[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10913969	0.81[CHB][hapmap];0.89[ASN][1000 genomes]
rs10913970	0.89[ASN][1000 genomes]
rs10913974	0.83[ASN][1000 genomes]
rs10913976	0.83[ASN][1000 genomes]
rs10913978	0.83[ASN][1000 genomes]
rs10913980	0.83[ASN][1000 genomes]
rs10913981	0.83[ASN][1000 genomes]
rs10913982	0.83[ASN][1000 genomes]
rs10913983	0.83[ASN][1000 genomes]
rs10913984	0.83[ASN][1000 genomes]
rs10913985	0.81[ASN][1000 genomes]
rs10913986	0.83[ASN][1000 genomes]
rs10913987	0.83[ASN][1000 genomes]
rs10913994	0.82[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10913998	0.81[ASN][1000 genomes]
rs10914001	0.82[ASN][1000 genomes]
rs10914002	0.88[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10914007	0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10914014	0.80[ASN][1000 genomes]
rs12024156	0.83[ASN][1000 genomes]
rs12034217	0.83[ASN][1000 genomes]
rs12034669	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12039933	0.82[CHB][hapmap];0.91[ASN][1000 genomes]
rs12045123	0.91[ASN][1000 genomes]
rs12045636	0.95[ASN][1000 genomes]
rs12085808	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12091722	0.81[CHB][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12122338	0.82[ASN][1000 genomes]
rs12127886	0.82[ASN][1000 genomes]
rs12128560	0.82[ASN][1000 genomes]
rs12129511	0.82[ASN][1000 genomes]
rs12129784	0.83[ASN][1000 genomes]
rs12131071	0.82[ASN][1000 genomes]
rs12132837	0.80[ASN][1000 genomes]
rs12135463	0.82[ASN][1000 genomes]
rs12142124	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12402815	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12403665	0.93[ASN][1000 genomes]
rs12404209	0.82[CHB][hapmap];0.89[ASN][1000 genomes]
rs12405902	0.82[CHB][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12407122	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12691484	0.88[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.80[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12730889	0.82[ASN][1000 genomes]
rs1341924	0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1418102	0.88[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1418103	0.85[CEU][hapmap]
rs1890731	0.82[ASN][1000 genomes]
rs1925339	0.83[CHB][hapmap]
rs2794962	0.82[CHB][hapmap]
rs2794978	0.91[EUR][1000 genomes]
rs28506072	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2877399	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2877415	0.82[CHB][hapmap];0.81[YRI][hapmap];0.91[ASN][1000 genomes]
rs3737584	0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs3806300	0.84[ASN][1000 genomes]
rs3923222	0.82[ASN][1000 genomes]
rs4058058	0.83[CHB][hapmap]
rs4076403	0.83[ASN][1000 genomes]
rs4142992	0.82[ASN][1000 genomes]
rs4418555	0.80[ASN][1000 genomes]
rs4420052	0.83[ASN][1000 genomes]
rs4421553	0.83[ASN][1000 genomes]
rs4436345	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4442335	0.81[ASN][1000 genomes]
rs4483365	0.88[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4543756	0.93[ASN][1000 genomes]
rs4562579	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4578179	0.83[ASN][1000 genomes]
rs4593778	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4607831	0.82[ASN][1000 genomes]
rs4634864	0.83[ASN][1000 genomes]
rs4642852	0.87[CHB][hapmap];0.90[JPT][hapmap];1.00[ASN][1000 genomes]
rs4651064	0.82[ASN][1000 genomes]
rs4652495	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4652496	0.89[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652498	0.88[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652499	0.89[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652505	0.81[ASN][1000 genomes]
rs55874160	1.00[ASN][1000 genomes]
rs60286873	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6425625	0.88[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425634	0.82[CHB][hapmap];0.93[ASN][1000 genomes]
rs6657492	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6658310	0.89[CEU][hapmap];0.96[EUR][1000 genomes]
rs6659513	1.00[ASN][1000 genomes]
rs6661208	0.81[CHB][hapmap];0.90[JPT][hapmap];1.00[ASN][1000 genomes]
rs6670544	0.82[ASN][1000 genomes]
rs6674244	0.82[ASN][1000 genomes]
rs6678216	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6680368	0.88[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6700986	0.82[ASN][1000 genomes]
rs72720915	0.83[ASN][1000 genomes]
rs72720917	0.83[ASN][1000 genomes]
rs7523003	0.81[ASN][1000 genomes]
rs7523857	0.82[ASN][1000 genomes]
rs7526189	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7528650	0.82[ASN][1000 genomes]
rs7532806	0.83[ASN][1000 genomes]
rs7538219	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7538303	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7539910	0.89[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7544585	1.00[ASN][1000 genomes]
rs822706	0.89[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9425497	0.94[EUR][1000 genomes]
rs9425878	0.90[EUR][1000 genomes]
rs9425880	0.94[EUR][1000 genomes]
rs9701037	0.84[ASN][1000 genomes]
rs9729819	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003739	chr1:180027760-180483292	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv535217	chr1:180027760-180483292	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv527918	chr1:180279710-180443808	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1013716	chr1:180287338-180477072	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
5	nsv535221	chr1:180287338-180477072	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
6	esv2762200	chr1:180300936-180493841	ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
7	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
8	nsv1014937	chr1:180360900-180399555	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180341200-180401400	Weak transcription	Osteobl	bone
2	chr1:180349400-180407000	Weak transcription	Esophagus	oesophagus
3	chr1:180352800-180399400	Weak transcription	Fetal Thymus	thymus
4	chr1:180355200-180402600	Weak transcription	HMEC	breast
5	chr1:180356600-180394000	Weak transcription	NHDF-Ad	bronchial
6	chr1:180356800-180406200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:180356800-180407000	Weak transcription	Aorta	Aorta
8	chr1:180360400-180394200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:180361400-180407600	Weak transcription	HepG2	liver
10	chr1:180364000-180394200	Weak transcription	HSMMtube	muscle
11	chr1:180364400-180401600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr1:180364600-180401000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:180365000-180401000	Weak transcription	Ovary	ovary
14	chr1:180365200-180420600	Weak transcription	A549	lung
15	chr1:180365400-180402600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:180366600-180393600	Weak transcription	NH-A	brain
17	chr1:180366800-180394000	Weak transcription	Fetal Lung	lung
18	chr1:180371200-180394400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr1:180374600-180394200	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr1:180374600-180404000	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr1:180374800-180394000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr1:180374800-180394000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr1:180376200-180407400	Weak transcription	NHLF	lung
24	chr1:180376800-180395800	Weak transcription	Colon Smooth Muscle	Colon
25	chr1:180377000-180394200	Weak transcription	Gastric	stomach
26	chr1:180379000-180430800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:180379400-180393600	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr1:180379400-180394000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr1:180379800-180406000	Weak transcription	Left Ventricle	heart
30	chr1:180380200-180396800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:180380400-180401000	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr1:180380400-180408000	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr1:180381200-180393400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr1:180381200-180393600	Weak transcription	Duodenum Mucosa	Duodenum
35	chr1:180381200-180402800	Weak transcription	NHEK	skin
36	chr1:180381200-180406400	Weak transcription	Fetal Stomach	stomach
37	chr1:180381400-180401000	Weak transcription	HSMM	muscle
38	chr1:180381800-180393400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr1:180381800-180397600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr1:180382400-180401000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr1:180382400-180410800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr1:180382600-180394000	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr1:180382600-180394000	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr1:180382600-180398600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:180382600-180400800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr1:180382600-180402800	Weak transcription	Placenta	Placenta
47	chr1:180382600-180406000	Weak transcription	Dnd41	blood
48	chr1:180382600-180406400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr1:180382600-180406600	Weak transcription	Hela-S3	cervix
50	chr1:180383600-180398400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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