Variant report

Variant	rs10498811
Chromosome Location	chr6:56561273-56561274
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:56561249-56561299	HCT-116	colon:	n/a
2	chr6:56561249-56561299	HIPEpiC	eye:	n/a
3	chr6:56561249-56561299	MCF-7	breast:	n/a
4	chr6:56561249-56561299	GM12891	blood:	n/a
5	chr6:56561249-56561299	GM06990	blood:	n/a
6	chr6:56561249-56561299	SAEC	small airway:	n/a
7	chr6:56561249-56561299	MCF10A-Er-Src	breast:	n/a
8	chr6:56561249-56561299	H1-hESC	embryonic stem cell:	embryo
9	chr6:56561249-56561299	GM12878	blood:	n/a
10	chr6:56561249-56561299	T-47D	breast:	n/a
11	chr6:56561249-56561299	HPAEpiC	pulmonary alveolar:	n/a
12	chr6:56561249-56561299	AG10803	skin:	n/a
13	chr6:56561249-56561299	IMR90	lung:	fetal
14	chr6:56561249-56561299	A549	lung:	n/a
15	chr6:56561249-56561299	HUVEC	blood vessel:	n/a
16	chr6:56561249-56561299	HMEC	breast:	n/a
17	chr6:56561249-56561299	RPTEC	kidney:	n/a
18	chr6:56561249-56561299	HRE	kidney:	n/a
19	chr6:56561249-56561299	K562	blood:	n/a
20	chr6:56561249-56561299	HL-60	blood:	n/a
21	chr6:56561249-56561299	Hela-S3	cervix:	n/a
22	chr6:56561249-56561299	GM12892	blood:	n/a
23	chr6:56561249-56561299	AG09309	skin:	n/a
24	chr6:56561249-56561299	HEK293	kidney:	embryo
25	chr6:56561249-56561299	HEEpiC	esophagus:	n/a
26	chr6:56561249-56561299	HCM	heart:	n/a
27	chr6:56561249-56561299	LNCaP	prostate:	n/a
28	chr6:56561249-56561299	PFSK-1	brain:	n/a
29	chr6:56561249-56561299	CMK	blood:	n/a
30	chr6:56561249-56561299	SK-N-SH_RA	brain:	n/a
31	chr6:56561249-56561299	ProgFib	skin:	n/a
32	chr6:56561249-56561299	Caco-2	colon:	n/a
33	chr6:56561249-56561299	NH-A	brain:	n/a
34	chr6:56561249-56561299	GM19239	blood:	n/a
35	chr6:56561249-56561299	Jurkat	blood:	n/a
36	chr6:56561249-56561299	AG09319	gingival:	n/a
37	chr6:56561249-56561299	AG04449	skin:	fetal
38	chr6:56561249-56561299	SK-N-MC	brain:	n/a
39	chr6:56561249-56561299	PrEC	prostate:	n/a
40	chr6:56561249-56561299	HRPEpiC	eye:	n/a
41	chr6:56561249-56561299	SKMC	muscle:	n/a
42	chr6:56561249-56561299	PANC-1	pancreas:	n/a
43	chr6:56561249-56561299	HRCEpiC	kidney:	n/a
44	chr6:56561249-56561299	NHBE	bronchial:	n/a
45	chr6:56561249-56561299	NB4	blood:	n/a
46	chr6:56561249-56561299	NT2-D1	testis:	n/a
47	chr6:56561249-56561299	ovcar-3	ovarian:	n/a
48	chr6:56561249-56561299	ECC-1	luminal epithelium:	n/a
49	chr6:56561249-56561299	AG04450	lung:	fetal
50	chr6:56561249-56561299	U87	brain:	n/a

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:56558539..56560309-chr6:56560912..56563103,2	MCF-7	breast:
2	chr6:56559575..56561733-chr6:56563230..56565614,2	MCF-7	breast:

No data

Variant related genes	Relation type
DST	CpG island

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs11961141	0.83[EUR][1000 genomes]
rs11961342	0.85[EUR][1000 genomes]
rs11968575	0.83[EUR][1000 genomes]
rs13191164	1.00[EUR][1000 genomes]
rs13192037	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13192478	0.83[EUR][1000 genomes]
rs13192567	0.83[EUR][1000 genomes]
rs13196211	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13198399	0.83[EUR][1000 genomes]
rs13198938	0.83[EUR][1000 genomes]
rs13203000	0.83[EUR][1000 genomes]
rs13205013	1.00[EUR][1000 genomes]
rs13206849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13210876	0.83[EUR][1000 genomes]
rs13213878	0.83[EUR][1000 genomes]
rs13217390	0.83[EUR][1000 genomes]
rs13219546	0.83[EUR][1000 genomes]
rs13219942	0.85[EUR][1000 genomes]
rs16888118	1.00[EUR][1000 genomes]
rs16888124	1.00[EUR][1000 genomes]
rs16888126	0.97[EUR][1000 genomes]
rs16888128	0.98[EUR][1000 genomes]
rs16888130	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs16888133	0.97[EUR][1000 genomes]
rs16888135	0.83[EUR][1000 genomes]
rs17684511	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17684553	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17684571	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17751682	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17751695	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2967960	0.82[EUR][1000 genomes]
rs2967963	0.81[EUR][1000 genomes]
rs3002003	0.83[EUR][1000 genomes]
rs3002004	0.83[EUR][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	0.83[EUR][1000 genomes]
rs3002011	0.83[EUR][1000 genomes]
rs34138864	1.00[EUR][1000 genomes]
rs34429594	0.84[EUR][1000 genomes]
rs34455199	0.83[EUR][1000 genomes]
rs34465210	0.83[EUR][1000 genomes]
rs34566275	0.83[EUR][1000 genomes]
rs34576803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34587484	0.83[EUR][1000 genomes]
rs34623351	0.83[EUR][1000 genomes]
rs34724718	1.00[EUR][1000 genomes]
rs34803237	0.83[EUR][1000 genomes]
rs34812826	0.83[EUR][1000 genomes]
rs34824960	0.83[EUR][1000 genomes]
rs34832779	0.82[EUR][1000 genomes]
rs35206656	0.98[EUR][1000 genomes]
rs35326806	0.85[EUR][1000 genomes]
rs35408048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35494794	0.85[EUR][1000 genomes]
rs35619924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35637749	1.00[EUR][1000 genomes]
rs35668437	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35687635	0.98[EUR][1000 genomes]
rs35876418	0.83[EUR][1000 genomes]
rs35920751	0.83[EUR][1000 genomes]
rs36068365	0.85[EUR][1000 genomes]
rs4072271	0.98[EUR][1000 genomes]
rs4073960	0.95[EUR][1000 genomes]
rs4074101	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4074102	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4074103	0.94[CEU][hapmap];0.97[EUR][1000 genomes]
rs41267675	0.83[EUR][1000 genomes]
rs4262190	0.91[EUR][1000 genomes]
rs4275049	0.83[EUR][1000 genomes]
rs4640889	0.83[EUR][1000 genomes]
rs5024547	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55742092	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56101897	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59085778	0.83[EUR][1000 genomes]
rs59247267	0.83[EUR][1000 genomes]
rs60498201	0.83[EUR][1000 genomes]
rs62412526	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62412528	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62412531	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62412532	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62412556	0.83[EUR][1000 genomes]
rs6901176	1.00[EUR][1000 genomes]
rs6924375	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6926134	0.83[EUR][1000 genomes]
rs6938003	0.82[EUR][1000 genomes]
rs71564848	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71564849	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7767128	1.00[CEU][hapmap];1.00[EUR][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	chr6:56547400-56561600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:56549600-56573600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr6:56549800-56578000	Weak transcription	Gastric	stomach
5	chr6:56554000-56574600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr6:56555400-56574600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr6:56555800-56561800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:56555800-56573600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr6:56556000-56568400	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr6:56556200-56573600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr6:56556200-56574400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr6:56556400-56561800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:56556400-56568000	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr6:56558200-56561800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr6:56558200-56562000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr6:56558200-56563400	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr6:56558200-56563600	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr6:56558200-56569800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr6:56558200-56573400	Weak transcription	Stomach Mucosa	stomach
20	chr6:56558200-56578200	Weak transcription	Aorta	Aorta
21	chr6:56558400-56561800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr6:56558400-56561800	Weak transcription	Psoas Muscle	Psoas
23	chr6:56558400-56561800	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr6:56558400-56562200	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr6:56558400-56562400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr6:56558400-56563400	Weak transcription	Brain Angular Gyrus	brain
27	chr6:56558400-56563600	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr6:56558400-56563600	Weak transcription	Stomach Smooth Muscle	stomach
29	chr6:56558400-56566400	Weak transcription	Colon Smooth Muscle	Colon
30	chr6:56558400-56567000	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr6:56558400-56571600	Weak transcription	Fetal Stomach	stomach
32	chr6:56558400-56573200	Weak transcription	Adipose Nuclei	Adipose
33	chr6:56558400-56577800	Weak transcription	Ovary	ovary
34	chr6:56558400-56579400	Weak transcription	Right Ventricle	heart
35	chr6:56558600-56562000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr6:56558600-56566400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr6:56558600-56577800	Weak transcription	Fetal Heart	heart
38	chr6:56559200-56563000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr6:56559400-56562000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr6:56559400-56563000	Strong transcription	HSMMtube	muscle
41	chr6:56559400-56563800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr6:56559600-56562600	Weak transcription	Liver	Liver
43	chr6:56559600-56563200	Strong transcription	HSMM	muscle
44	chr6:56559600-56572600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr6:56559600-56573000	Weak transcription	NH-A	brain
46	chr6:56559800-56577800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr6:56560000-56561400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr6:56560000-56562200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr6:56560200-56562200	Genic enhancers	Osteobl	bone
50	chr6:56560200-56579800	Weak transcription	Fetal Muscle Leg	muscle

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