Variant report

Variant	rs6657968
Chromosome Location	chr1:228384956-228384957
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228372145..228374632-chr1:228384482..228386593,2	K562	blood:
2	chr1:228382588..228385276-chr1:228392275..228394385,3	MCF-7	breast:
3	chr1:228352906..228354898-chr1:228384251..228386544,2	K562	blood:
4	chr1:228362968..228364679-chr1:228382995..228385252,2	K562	blood:

Variant related genes	Relation type
ENSG00000181873	Chromatin interaction
ENSG00000203684	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1059778	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs10753445	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs10916271	0.81[EUR][1000 genomes]
rs10916277	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11584385	0.84[CEU][hapmap]
rs12084338	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12097591	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12130630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12134624	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12745416	0.85[CEU][hapmap]
rs1411910	0.84[CEU][hapmap]
rs1411911	0.89[EUR][1000 genomes]
rs1557026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1620111	0.84[CEU][hapmap]
rs1629294	0.84[CEU][hapmap]
rs1757132	0.85[CEU][hapmap]
rs1757133	0.85[CEU][hapmap]
rs1757139	0.84[CEU][hapmap]
rs1757147	0.84[CEU][hapmap]
rs1757149	0.84[CEU][hapmap]
rs1757150	0.82[CEU][hapmap]
rs1757152	0.84[CEU][hapmap]
rs1757156	0.84[CEU][hapmap]
rs17623766	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17640616	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1771459	0.84[CEU][hapmap]
rs1771460	0.84[CEU][hapmap]
rs1771461	0.81[CEU][hapmap]
rs1771462	0.84[CEU][hapmap]
rs1771467	0.84[CEU][hapmap]
rs1771472	0.84[CEU][hapmap]
rs1771474	0.84[CEU][hapmap]
rs1771476	0.85[CEU][hapmap]
rs1771479	0.81[CEU][hapmap]
rs1771482	0.84[CEU][hapmap]
rs1771483	0.82[CEU][hapmap]
rs1771484	0.92[CEU][hapmap]
rs1771485	0.85[CEU][hapmap]
rs1771487	0.81[CEU][hapmap]
rs2066237	0.84[CEU][hapmap]
rs2185544	0.82[EUR][1000 genomes]
rs2298014	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2313600	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2313601	0.84[CEU][hapmap]
rs2313602	0.84[CEU][hapmap]
rs2776855	0.84[CEU][hapmap]
rs2776856	0.84[CEU][hapmap]
rs2872538	0.84[CEU][hapmap]
rs3845621	0.85[YRI][hapmap]
rs4653536	0.80[EUR][1000 genomes]
rs4653907	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4653917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4653919	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4653920	0.96[EUR][1000 genomes]
rs4653921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55658545	0.90[EUR][1000 genomes]
rs55873533	0.91[EUR][1000 genomes]
rs61825279	0.86[EUR][1000 genomes]
rs6426492	0.96[CEU][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs6661539	0.89[EUR][1000 genomes]
rs6673893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6676755	0.88[YRI][hapmap]
rs6682260	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6704220	0.90[YRI][hapmap]
rs708123	0.86[YRI][hapmap]
rs72757811	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72757812	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72757824	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72757827	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72757829	0.93[EUR][1000 genomes]
rs7512209	0.84[CEU][hapmap]
rs752107	1.00[YRI][hapmap]
rs7532141	0.88[EUR][1000 genomes]
rs7532924	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs7537636	0.84[CEU][hapmap]
rs7539762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs766972	1.00[YRI][hapmap]
rs947087	0.84[CEU][hapmap]
rs9728319	0.93[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
3	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
5	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
6	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
7	nsv827019	chr1:228314167-228651020	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
8	nsv873257	chr1:228322826-228412106	Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
9	nsv1012078	chr1:228340876-228521843	Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
10	nsv535320	chr1:228340876-228521843	Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
11	esv1808523	chr1:228359177-228400358	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6657968	IBA57	cis	Whole Blood	GTEx
rs6657968	OBSCN	cis	Esophagus Mucosa	GTEx
rs6657968	OBSCN	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228354600-228385200	Weak transcription	Left Ventricle	heart
2	chr1:228363400-228386400	Weak transcription	Brain Angular Gyrus	brain
3	chr1:228363800-228385200	Weak transcription	Adipose Nuclei	Adipose
4	chr1:228364400-228386600	Weak transcription	Brain Hippocampus Middle	brain
5	chr1:228364400-228388600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:228364600-228386600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr1:228364800-228385600	Weak transcription	Brain Anterior Caudate	brain
8	chr1:228365200-228386600	Weak transcription	Thymus	Thymus
9	chr1:228365200-228387800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:228366000-228386400	Weak transcription	Primary B cells from cord blood	blood
11	chr1:228366800-228385200	Weak transcription	Ovary	ovary
12	chr1:228366800-228386600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr1:228366800-228393400	Weak transcription	Right Ventricle	heart
14	chr1:228371200-228386400	Weak transcription	Primary T cells from cord blood	blood
15	chr1:228373800-228386200	Weak transcription	Fetal Stomach	stomach
16	chr1:228373800-228394000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr1:228376400-228385200	Weak transcription	Fetal Brain Female	brain
18	chr1:228380400-228386400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:228380800-228385000	Weak transcription	Fetal Muscle Leg	muscle
20	chr1:228381200-228385000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr1:228381400-228386400	Weak transcription	Fetal Heart	heart
22	chr1:228382600-228393000	Weak transcription	Colonic Mucosa	Colon
23	chr1:228383200-228386400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr1:228383200-228394600	Weak transcription	Fetal Brain Male	brain
25	chr1:228384600-228385400	Enhancers	Psoas Muscle	Psoas
26	chr1:228384600-228385600	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr1:228384600-228386000	Enhancers	Fetal Muscle Trunk	muscle

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