Variant report

Variant	rs4653849
Chromosome Location	chr1:227729000-227729001
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:227727749..227729472-chr1:227739111..227740675,2	K562	blood:
2	chr1:227721537..227724263-chr1:227727527..227730135,2	MCF-7	breast:
3	chr1:227725139..227726773-chr1:227727190..227729662,2	K562	blood:
4	chr1:227725436..227728346-chr1:227728933..227731230,4	MCF-7	breast:
5	chr1:227728970..227731707-chr1:227751101..227754291,3	MCF-7	breast:
6	chr1:227727960..227729815-chr1:228131832..228133962,2	MCF-7	breast:
7	chr1:227728158..227729940-chr1:227914897..227917653,2	MCF-7	breast:
8	chr1:227728577..227730296-chr1:227730401..227732480,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000143740	Chromatin interaction
ENSG00000181450	Chromatin interaction

Extended variants
information (count: 118 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10047205	0.86[JPT][hapmap]
rs1021553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1021554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10495276	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10799423	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10799431	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10799432	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10799433	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10799434	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10799435	1.00[CEU][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10916158	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916159	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10916165	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10916169	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10916175	0.91[EUR][1000 genomes]
rs10916176	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10916178	0.81[JPT][hapmap]
rs10916179	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10916182	1.00[CEU][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10916183	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10916184	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10916185	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10916187	1.00[CEU][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11484723	0.87[EUR][1000 genomes]
rs11580570	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12023298	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12025815	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12040302	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12070002	1.00[CEU][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12070036	1.00[CEU][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12079123	0.91[EUR][1000 genomes]
rs12080321	1.00[CEU][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12080590	0.82[JPT][hapmap]
rs12082414	0.82[JPT][hapmap]
rs12096675	0.86[JPT][hapmap]
rs12132444	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12740317	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1407718	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1495842	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1495845	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1495847	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1495849	0.91[JPT][hapmap]
rs16847966	0.82[JPT][hapmap]
rs16847991	0.82[JPT][hapmap]
rs16847992	0.82[JPT][hapmap]
rs16848029	0.86[JPT][hapmap]
rs1845758	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2018401	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2088210	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2088211	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2088212	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2088214	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2093609	1.00[CEU][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2093610	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2132366	0.82[JPT][hapmap]
rs2132367	1.00[CEU][hapmap];0.80[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2201571	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2453682	0.87[JPT][hapmap]
rs2644140	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2644161	0.87[JPT][hapmap]
rs28407112	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2935145	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2935146	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2935147	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2935152	1.00[CEU][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2935155	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2999741	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2999743	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2999744	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2999745	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2999746	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3010183	1.00[CEU][hapmap];0.80[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3010186	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3010190	1.00[CEU][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3010191	1.00[CEU][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3010192	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3010193	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3010194	1.00[CEU][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3010195	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3010196	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3748806	0.86[JPT][hapmap]
rs4359006	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4376731	0.86[JPT][hapmap]
rs4653512	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4653514	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4653515	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4653848	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653850	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4653853	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6664682	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6671825	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6683151	1.00[CEU][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap]
rs6697867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7512348	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7523915	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7528094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7539151	0.86[JPT][hapmap]
rs7539914	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7542685	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7551459	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs903683	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs903684	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs903690	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs903694	0.91[JPT][hapmap]
rs903695	0.91[JPT][hapmap]
rs903697	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs951083	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs965942	0.82[JPT][hapmap]
rs976959	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	esv2753828	chr1:227670265-227791265	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv873244	chr1:227682414-227736363	Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv873246	chr1:227694948-227884465	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
6	nsv873247	chr1:227697381-227736363	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv873248	chr1:227710381-227786033	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv947520	chr1:227724042-227750192	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv947560	chr1:227726600-227750192	ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4653849	ZNF678	cis	cerebellum	SCAN
rs4653849	SNAP47	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227720800-227729200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:227720800-227729200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:227725200-227729000	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr1:227726200-227729600	Weak transcription	Aorta	Aorta
5	chr1:227726400-227729200	Weak transcription	Liver	Liver
6	chr1:227728000-227729200	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr1:227728400-227729200	Enhancers	Duodenum Mucosa	Duodenum
8	chr1:227728400-227729600	Enhancers	Spleen	Spleen
9	chr1:227728600-227729200	Weak transcription	Gastric	stomach
10	chr1:227728600-227729400	Enhancers	Pancreas	Pancrea
11	chr1:227728800-227729000	Enhancers	Stomach Smooth Muscle	stomach
12	chr1:227728800-227730400	Active TSS	Brain Anterior Caudate	brain
13	chr1:227729000-227729200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:227729000-227729200	Enhancers	Adipose Nuclei	Adipose
15	chr1:227729000-227729200	Enhancers	Brain Angular Gyrus	brain
16	chr1:227729000-227729200	Enhancers	Brain Cingulate Gyrus	brain
17	chr1:227729000-227729200	Enhancers	Brain Hippocampus Middle	brain
18	chr1:227729000-227729200	Enhancers	Brain Substantia Nigra	brain
19	chr1:227729000-227729200	Enhancers	Lung	lung
20	chr1:227729000-227729200	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr1:227729000-227729200	Enhancers	Osteobl	bone
22	chr1:227729000-227729400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr1:227729000-227729400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
24	chr1:227729000-227729800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
25	chr1:227729000-227729800	Flanking Active TSS	Stomach Smooth Muscle	stomach

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