Variant report

Variant	rs16888118
Chromosome Location	chr6:56552636-56552637
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 141 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:137)

rs_ID	r²[population]
rs1024196	1.00[CHD][hapmap];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	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11966986	1.00[ASN][1000 genomes]
rs11967796	1.00[ASN][1000 genomes]
rs11968575	1.00[CHD][hapmap];0.85[GIH][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11970410	0.90[ASN][1000 genomes]
rs11970648	1.00[CHD][hapmap];0.87[LWK][hapmap];0.80[MKK][hapmap];0.82[YRI][hapmap]
rs13190784	1.00[CHD][hapmap]
rs13191164	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13192037	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs13192478	0.85[AFR][1000 genomes];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	0.81[AFR][1000 genomes];0.90[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	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13217390	0.83[EUR][1000 genomes]
rs13219546	0.82[AFR][1000 genomes];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]
rs16888124	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888126	0.97[EUR][1000 genomes]
rs16888128	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888130	1.00[CEU][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888133	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888135	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16888171	1.00[CHD][hapmap]
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[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17751695	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1903332	1.00[CHD][hapmap]
rs2144407	1.00[ASN][1000 genomes]
rs2180148	1.00[ASN][1000 genomes]
rs2967960	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2967963	0.81[EUR][1000 genomes]
rs3002003	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3002004	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3002006	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3002007	0.81[EUR][1000 genomes]
rs3002008	0.83[EUR][1000 genomes]
rs3002009	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3002010	0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3002011	0.80[YRI][hapmap];0.83[EUR][1000 genomes]
rs34138864	0.85[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]
rs34703847	0.84[AFR][1000 genomes]
rs34724718	0.83[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	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34832779	0.82[EUR][1000 genomes]
rs35089136	0.89[ASN][1000 genomes]
rs35206656	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	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35668437	1.00[EUR][1000 genomes]
rs35687635	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35876418	0.83[EUR][1000 genomes]
rs35920751	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36068365	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4072271	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4073960	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4074101	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4074102	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs4074103	0.94[CEU][hapmap];0.81[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs41267673	1.00[ASN][1000 genomes]
rs41267675	0.83[EUR][1000 genomes]
rs4133076	1.00[ASN][1000 genomes]
rs4262190	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4275049	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4574644	0.89[ASN][1000 genomes]
rs4640889	0.82[AFR][1000 genomes];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	0.87[AFR][1000 genomes];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	0.98[AFR][1000 genomes];0.91[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]
rs6924375	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6926134	0.83[AFR][1000 genomes];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[CHD][hapmap];1.00[ASN][1000 genomes]
rs7749437	1.00[ASN][1000 genomes]
rs7758867	1.00[CHD][hapmap]
rs7759479	0.81[LWK][hapmap];1.00[ASN][1000 genomes]
rs7760503	1.00[ASN][1000 genomes]
rs7760542	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs7761027	1.00[ASN][1000 genomes]
rs7767128	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7775134	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv432888	chr6:56507489-56560764	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56527000-56554400	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr6:56529600-56553800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr6:56535200-56555200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr6:56537200-56553400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr6:56537200-56555200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:56537600-56553600	Weak transcription	Fetal Stomach	stomach
7	chr6:56543000-56559400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:56545600-56553400	Enhancers	Brain Hippocampus Middle	brain
9	chr6:56546200-56564800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr6:56546800-56555400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr6:56547200-56553400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr6:56547200-56554000	Enhancers	Brain Cingulate Gyrus	brain
13	chr6:56547200-56557400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr6:56547400-56552800	Enhancers	Brain Anterior Caudate	brain
15	chr6:56547400-56561600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:56548800-56553000	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr6:56548800-56554000	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr6:56549000-56553400	Weak transcription	Small Intestine	intestine
19	chr6:56549000-56553800	Weak transcription	Adipose Nuclei	Adipose
20	chr6:56549400-56553400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:56549400-56553400	Weak transcription	Hela-S3	cervix
22	chr6:56549400-56553400	Weak transcription	NHEK	skin
23	chr6:56549400-56553600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr6:56549600-56552800	Weak transcription	Colon Smooth Muscle	Colon
25	chr6:56549600-56552800	Weak transcription	Duodenum Mucosa	Duodenum
26	chr6:56549600-56553400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr6:56549600-56553600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr6:56549600-56553600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr6:56549600-56553600	Weak transcription	Colonic Mucosa	Colon
30	chr6:56549600-56553600	Enhancers	HepG2	liver
31	chr6:56549600-56554200	Weak transcription	NH-A	brain
32	chr6:56549600-56554400	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr6:56549600-56554600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr6:56549600-56554600	Weak transcription	HUVEC	blood vessel
35	chr6:56549600-56558000	Weak transcription	HMEC	breast
36	chr6:56549600-56573600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr6:56549800-56553400	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr6:56549800-56553400	Weak transcription	GM12878-XiMat	blood
39	chr6:56549800-56554200	Weak transcription	Fetal Muscle Leg	muscle
40	chr6:56549800-56555200	Weak transcription	Fetal Heart	heart
41	chr6:56549800-56555200	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr6:56549800-56578000	Weak transcription	Gastric	stomach
43	chr6:56550400-56553200	Enhancers	NHDF-Ad	bronchial
44	chr6:56550400-56553600	Weak transcription	Aorta	Aorta
45	chr6:56550400-56554400	Enhancers	Pancreatic Islets	Pancreatic Islet
46	chr6:56550400-56555400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr6:56550600-56553600	Weak transcription	Psoas Muscle	Psoas
48	chr6:56550600-56555200	Genic enhancers	HSMM	muscle
49	chr6:56550800-56553000	Genic enhancers	Muscle Satellite Cultured Cells	--
50	chr6:56550800-56554800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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