Variant report

Variant	rs6924375
Chromosome Location	chr6:56561791-56561792
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr6:56561506-56562105	HepG2	liver:	n/a	n/a
2	POLR2A	chr6:56561759-56561965	A549	lung:	n/a	n/a
3	CEBPB	chr6:56561777-56562088	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:56558539..56560309-chr6:56560912..56563103,2	MCF-7	breast:
2	chr6:56504038..56506002-chr6:56561278..56563980,2	MCF-7	breast:

Variant related genes	Relation type
DST	TF binding region

Extended variants
information (count: 133 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs1024196	1.00[ASN][1000 genomes]
rs10498811	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11961141	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11961342	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11966986	1.00[ASN][1000 genomes]
rs11967796	1.00[ASN][1000 genomes]
rs11968575	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11970410	0.90[ASN][1000 genomes]
rs13191164	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13192037	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs13192478	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13192567	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13196211	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs13198399	0.83[EUR][1000 genomes]
rs13198938	0.83[EUR][1000 genomes]
rs13203000	0.83[EUR][1000 genomes]
rs13205013	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13206849	1.00[EUR][1000 genomes]
rs13210876	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13213878	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13217390	0.83[EUR][1000 genomes]
rs13219546	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13219942	0.85[EUR][1000 genomes]
rs16888085	0.90[ASN][1000 genomes]
rs16888096	1.00[ASN][1000 genomes]
rs16888106	1.00[ASN][1000 genomes]
rs16888118	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888124	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888126	0.97[EUR][1000 genomes]
rs16888128	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888130	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888133	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888135	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17684511	1.00[EUR][1000 genomes]
rs17684553	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs17684571	0.98[EUR][1000 genomes]
rs17751682	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17751695	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2144407	1.00[ASN][1000 genomes]
rs2180148	1.00[ASN][1000 genomes]
rs2967960	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2967963	0.81[EUR][1000 genomes]
rs3002003	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3002004	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3002006	0.83[EUR][1000 genomes]
rs3002007	0.81[EUR][1000 genomes]
rs3002008	0.83[EUR][1000 genomes]
rs3002009	0.83[EUR][1000 genomes]
rs3002010	0.81[YRI][hapmap];0.83[EUR][1000 genomes]
rs3002011	0.83[EUR][1000 genomes]
rs34138864	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34429594	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34455199	0.83[EUR][1000 genomes]
rs34465210	0.83[EUR][1000 genomes]
rs34566275	0.83[EUR][1000 genomes]
rs34576803	0.98[EUR][1000 genomes]
rs34587484	0.83[EUR][1000 genomes]
rs34623351	0.83[EUR][1000 genomes]
rs34724718	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34803237	0.83[EUR][1000 genomes]
rs34812826	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34824960	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34832779	0.82[EUR][1000 genomes]
rs35089136	0.89[ASN][1000 genomes]
rs35206656	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35326806	0.85[EUR][1000 genomes]
rs35408048	1.00[EUR][1000 genomes]
rs35494794	0.85[EUR][1000 genomes]
rs35619924	1.00[EUR][1000 genomes]
rs35637749	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35668437	1.00[EUR][1000 genomes]
rs35687635	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35876418	0.83[EUR][1000 genomes]
rs35920751	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36068365	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4072271	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4073960	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4074101	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs4074102	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs4074103	0.94[CEU][hapmap];0.97[EUR][1000 genomes]
rs41267673	1.00[ASN][1000 genomes]
rs41267675	0.83[EUR][1000 genomes]
rs4133076	1.00[ASN][1000 genomes]
rs4262190	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4275049	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4574644	0.89[ASN][1000 genomes]
rs4640889	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5024547	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs55742092	0.97[EUR][1000 genomes]
rs56094263	0.89[ASN][1000 genomes]
rs56101897	1.00[EUR][1000 genomes]
rs56196625	1.00[ASN][1000 genomes]
rs57289287	1.00[ASN][1000 genomes]
rs57392123	1.00[ASN][1000 genomes]
rs57488435	1.00[ASN][1000 genomes]
rs58565063	1.00[ASN][1000 genomes]
rs59073430	1.00[ASN][1000 genomes]
rs59085778	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59162324	0.89[ASN][1000 genomes]
rs59247267	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59772940	1.00[ASN][1000 genomes]
rs59889120	1.00[ASN][1000 genomes]
rs60360551	1.00[ASN][1000 genomes]
rs60498201	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62412526	1.00[EUR][1000 genomes]
rs62412528	1.00[EUR][1000 genomes]
rs62412531	1.00[EUR][1000 genomes]
rs62412532	1.00[EUR][1000 genomes]
rs62412556	0.83[EUR][1000 genomes]
rs6459167	1.00[ASN][1000 genomes]
rs6459168	1.00[ASN][1000 genomes]
rs6900572	1.00[ASN][1000 genomes]
rs6901176	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6903815	1.00[ASN][1000 genomes]
rs6916813	1.00[ASN][1000 genomes]
rs6926134	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6938003	0.82[EUR][1000 genomes]
rs71564848	0.98[EUR][1000 genomes]
rs71564849	0.98[EUR][1000 genomes]
rs73746926	1.00[ASN][1000 genomes]
rs73746929	1.00[ASN][1000 genomes]
rs73746930	1.00[ASN][1000 genomes]
rs73746931	1.00[ASN][1000 genomes]
rs7749100	1.00[ASN][1000 genomes]
rs7749437	1.00[ASN][1000 genomes]
rs7759479	1.00[ASN][1000 genomes]
rs7760503	1.00[ASN][1000 genomes]
rs7760542	1.00[ASN][1000 genomes]
rs7761027	1.00[ASN][1000 genomes]
rs7767128	1.00[CEU][hapmap];0.97[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56546200-56564800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:56549600-56573600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr6:56549800-56578000	Weak transcription	Gastric	stomach
4	chr6:56554000-56574600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr6:56555400-56574600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr6:56555800-56561800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr6:56555800-56573600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr6:56556000-56568400	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr6:56556200-56573600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr6:56556200-56574400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:56556400-56561800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:56556400-56568000	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr6:56558200-56561800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr6:56558200-56562000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr6:56558200-56563400	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr6:56558200-56563600	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr6:56558200-56569800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr6:56558200-56573400	Weak transcription	Stomach Mucosa	stomach
19	chr6:56558200-56578200	Weak transcription	Aorta	Aorta
20	chr6:56558400-56561800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr6:56558400-56561800	Weak transcription	Psoas Muscle	Psoas
22	chr6:56558400-56561800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr6:56558400-56562200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr6:56558400-56562400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr6:56558400-56563400	Weak transcription	Brain Angular Gyrus	brain
26	chr6:56558400-56563600	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr6:56558400-56563600	Weak transcription	Stomach Smooth Muscle	stomach
28	chr6:56558400-56566400	Weak transcription	Colon Smooth Muscle	Colon
29	chr6:56558400-56567000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr6:56558400-56571600	Weak transcription	Fetal Stomach	stomach
31	chr6:56558400-56573200	Weak transcription	Adipose Nuclei	Adipose
32	chr6:56558400-56577800	Weak transcription	Ovary	ovary
33	chr6:56558400-56579400	Weak transcription	Right Ventricle	heart
34	chr6:56558600-56562000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr6:56558600-56566400	Weak transcription	Rectal Smooth Muscle	rectum
36	chr6:56558600-56577800	Weak transcription	Fetal Heart	heart
37	chr6:56559200-56563000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr6:56559400-56562000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr6:56559400-56563000	Strong transcription	HSMMtube	muscle
40	chr6:56559400-56563800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr6:56559600-56562600	Weak transcription	Liver	Liver
42	chr6:56559600-56563200	Strong transcription	HSMM	muscle
43	chr6:56559600-56572600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr6:56559600-56573000	Weak transcription	NH-A	brain
45	chr6:56559800-56577800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr6:56560000-56562200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr6:56560200-56562200	Genic enhancers	Osteobl	bone
48	chr6:56560200-56579800	Weak transcription	Fetal Muscle Leg	muscle
49	chr6:56560400-56561800	Weak transcription	Brain Hippocampus Middle	brain
50	chr6:56560400-56561800	Weak transcription	GM12878-XiMat	blood

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