Variant report

Variant	rs1772256
Chromosome Location	chr6:24437445-24437446
allele	A/G
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	POLR2A	chr6:24437332-24437511	MCF-7	breast:	n/a	n/a
2	MYC	chr6:24437437-24437539	MCF-7	breast:	n/a	n/a
3	POLR2A	chr6:24437429-24437669	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
GPLD1	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1042303	0.91[YRI][hapmap];0.81[AFR][1000 genomes]
rs2744549	1.00[CHD][hapmap]
rs2744550	1.00[CHD][hapmap]
rs2744559	1.00[CHD][hapmap]
rs2817191	1.00[CHD][hapmap]
rs2817195	1.00[CHD][hapmap]
rs3181759	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4472344	1.00[CHD][hapmap]
rs56148439	0.80[AMR][1000 genomes]
rs7744621	1.00[CHD][hapmap]
rs7744939	1.00[CHD][hapmap]
rs7749794	1.00[CHD][hapmap]
rs7751846	1.00[CEU][hapmap];1.00[CHD][hapmap];0.82[LWK][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7752186	1.00[CEU][hapmap];1.00[CHD][hapmap];0.82[LWK][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7752603	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[LWK][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7757601	1.00[CEU][hapmap]
rs7760171	1.00[CHD][hapmap]
rs7764860	1.00[CHD][hapmap]
rs7768124	1.00[CEU][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7770041	1.00[CHD][hapmap]
rs7772115	1.00[CEU][hapmap];1.00[CHD][hapmap];0.82[LWK][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7772540	1.00[CEU][hapmap];1.00[CHD][hapmap];0.82[LWK][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs793656	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap]
rs9461007	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9461008	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9461009	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9467136	1.00[CEU][hapmap]
rs9467142	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9467143	0.80[AFR][1000 genomes]
rs9467144	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9467145	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9467146	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9467147	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9467150	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9467151	1.00[CEU][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9467152	1.00[CEU][hapmap];0.80[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9467153	0.80[YRI][hapmap];0.80[AFR][1000 genomes]
rs9467154	1.00[CEU][hapmap];0.81[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026638	chr6:24347972-24475300	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24417400-24451800	Strong transcription	Liver	Liver
2	chr6:24421200-24448800	Weak transcription	Gastric	stomach
3	chr6:24421200-24459600	Weak transcription	Spleen	Spleen
4	chr6:24423400-24439400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr6:24424000-24456600	Weak transcription	Ovary	ovary
6	chr6:24424400-24445800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr6:24425400-24439600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr6:24426000-24438800	Weak transcription	Brain Substantia Nigra	brain
9	chr6:24426200-24446000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr6:24426400-24441600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr6:24426400-24446000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr6:24426600-24438800	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr6:24427600-24437600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr6:24427600-24439200	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr6:24427600-24439400	Weak transcription	Fetal Thymus	thymus
16	chr6:24427600-24440000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr6:24427600-24440000	Weak transcription	Dnd41	blood
18	chr6:24427600-24441800	Weak transcription	Primary B cells from peripheral blood	blood
19	chr6:24427600-24445600	Weak transcription	Fetal Brain Female	brain
20	chr6:24427600-24456800	Weak transcription	Lung	lung
21	chr6:24427800-24467000	Weak transcription	Brain Germinal Matrix	brain
22	chr6:24428200-24438000	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr6:24428200-24449400	Weak transcription	Fetal Muscle Trunk	muscle
24	chr6:24428800-24445000	Weak transcription	Psoas Muscle	Psoas
25	chr6:24429000-24447800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:24429000-24494200	Weak transcription	Primary B cells from cord blood	blood
27	chr6:24429200-24455600	Weak transcription	Brain Angular Gyrus	brain
28	chr6:24429400-24438600	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr6:24429400-24445000	Weak transcription	Brain Anterior Caudate	brain
30	chr6:24429400-24483800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr6:24429600-24444800	Weak transcription	HepG2	liver
32	chr6:24429600-24455000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr6:24430800-24448400	Weak transcription	Brain Hippocampus Middle	brain
34	chr6:24432600-24463800	Weak transcription	Fetal Intestine Small	intestine
35	chr6:24433200-24441600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr6:24433600-24451600	Weak transcription	Adipose Nuclei	Adipose
37	chr6:24435800-24438200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr6:24436200-24438400	Strong transcription	Primary T cells from cord blood	blood
39	chr6:24436200-24438600	Strong transcription	Fetal Stomach	stomach
40	chr6:24436200-24438600	Strong transcription	Stomach Smooth Muscle	stomach
41	chr6:24436600-24437800	Strong transcription	Brain Inferior Temporal Lobe	brain
42	chr6:24436600-24438000	Strong transcription	Thymus	Thymus
43	chr6:24436600-24438400	Strong transcription	Fetal Muscle Leg	muscle
44	chr6:24437000-24438200	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr6:24437200-24438000	Strong transcription	Pancreas	Pancrea
46	chr6:24437200-24438400	Strong transcription	Right Ventricle	heart
47	chr6:24437200-24438800	Strong transcription	Brain Cingulate Gyrus	brain
48	chr6:24437400-24437600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr6:24437400-24437600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr6:24437400-24437800	Strong transcription	Left Ventricle	heart

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