Variant report

Variant	rs6933328
Chromosome Location	chr6:24710920-24710921
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:24710064..24711659-chr6:24781117..24783754,2	K562	blood:
2	chr6:24701416..24703004-chr6:24710087..24712359,2	MCF-7	breast:
3	chr6:24709253..24711356-chr6:24713475..24715005,2	MCF-7	breast:
4	chr6:24703121..24705782-chr6:24707406..24711144,3	MCF-7	breast:
5	chr6:24697429..24699456-chr6:24708438..24711427,3	K562	blood:
6	chr6:24707645..24711659-chr6:24779375..24784848,6	K562	blood:

Variant related genes	Relation type
ENSG00000272345	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1053598	0.84[CEU][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs10946719	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1129644	0.81[CHD][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap]
rs1555086	0.80[EUR][1000 genomes]
rs1555087	0.84[JPT][hapmap]
rs1555088	0.84[JPT][hapmap];0.80[EUR][1000 genomes]
rs1885208	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1885209	0.80[EUR][1000 genomes]
rs1885210	0.80[EUR][1000 genomes]
rs1923186	0.80[ASN][1000 genomes]
rs2056999	0.81[CHD][hapmap];0.84[GIH][hapmap];0.84[JPT][hapmap]
rs2092404	1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2143337	0.81[CHD][hapmap];0.94[GIH][hapmap];0.84[JPT][hapmap]
rs2223588	0.81[CHD][hapmap];0.94[GIH][hapmap];0.84[JPT][hapmap]
rs3212233	0.82[JPT][hapmap]
rs3777664	0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3813685	0.80[ASN][1000 genomes]
rs3822901	0.81[CHD][hapmap];0.94[GIH][hapmap];0.80[EUR][1000 genomes]
rs4712839	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4712840	0.91[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6931502	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7764633	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7770027	0.82[EUR][1000 genomes]
rs926528	0.80[EUR][1000 genomes]
rs926529	0.81[CHD][hapmap];0.84[JPT][hapmap];0.80[EUR][1000 genomes]
rs9461049	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3508002	chr6:24618580-24732946	Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv3508003	chr6:24618580-24732946	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6933328	HIST1H3G	cis	cerebellum	SCAN
rs6933328	ACOT13	cis	cerebellum	SCAN
rs6933328	ZSCAN23	cis	cerebellum	SCAN
rs6933328	MRS2	cis	parietal	SCAN
rs6933328	TDP2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24697800-24715800	Strong transcription	Fetal Thymus	thymus
2	chr6:24698000-24711600	Strong transcription	Primary T cells from cord blood	blood
3	chr6:24698200-24716200	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr6:24698200-24716200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:24698200-24716400	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr6:24698200-24717400	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr6:24698400-24717400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
8	chr6:24698600-24715200	Weak transcription	Fetal Heart	heart
9	chr6:24698600-24716200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr6:24698600-24716200	Weak transcription	Right Atrium	heart
11	chr6:24699000-24716600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr6:24699000-24717400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:24699600-24712800	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr6:24699800-24712400	Strong transcription	Dnd41	blood
15	chr6:24700000-24716800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr6:24700200-24713200	Weak transcription	Stomach Mucosa	stomach
17	chr6:24700600-24712400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr6:24701000-24711400	Strong transcription	Brain Hippocampus Middle	brain
19	chr6:24701200-24711400	Strong transcription	Liver	Liver
20	chr6:24701200-24712200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr6:24701200-24713000	Strong transcription	Duodenum Smooth Muscle	Duodenum
22	chr6:24701200-24714200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr6:24701400-24711000	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr6:24701400-24711400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr6:24701400-24712200	Strong transcription	Duodenum Mucosa	Duodenum
26	chr6:24701400-24713000	Strong transcription	Primary B cells from cord blood	blood
27	chr6:24701400-24713000	Strong transcription	Primary hematopoietic stem cells	blood
28	chr6:24701400-24713200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr6:24701400-24713200	Strong transcription	Fetal Intestine Large	intestine
30	chr6:24701400-24715400	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr6:24701400-24716800	Strong transcription	Placenta	Placenta
32	chr6:24701600-24712000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr6:24701600-24712400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr6:24701600-24714800	Strong transcription	HUVEC	blood vessel
35	chr6:24701600-24716200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr6:24701600-24716200	Strong transcription	Stomach Smooth Muscle	stomach
37	chr6:24701600-24716200	Strong transcription	HMEC	breast
38	chr6:24701600-24716600	Strong transcription	Fetal Muscle Trunk	muscle
39	chr6:24701600-24716600	Strong transcription	Fetal Muscle Leg	muscle
40	chr6:24701800-24715400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr6:24701800-24715600	Strong transcription	Osteobl	bone
42	chr6:24701800-24716200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr6:24701800-24716800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr6:24702000-24712000	Strong transcription	NHEK	skin
45	chr6:24702200-24711000	Strong transcription	Brain Anterior Caudate	brain
46	chr6:24702200-24711200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr6:24702200-24711400	Strong transcription	Brain Germinal Matrix	brain
48	chr6:24702200-24714800	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr6:24702200-24715000	Strong transcription	NHLF	lung
50	chr6:24702200-24716400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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