Variant report

Variant	rs793683
Chromosome Location	chr6:24430292-24430293
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:24421995..24424017-chr6:24428873..24431634,2	K562	blood:
2	chr6:24426316..24427953-chr6:24428203..24431025,2	MCF-7	breast:
3	chr6:24429196..24431660-chr6:24699102..24701042,2	MCF-7	breast:
4	chr6:24429052..24430696-chr6:24494120..24495695,2	MCF-7	breast:
5	chr6:24413201..24415525-chr6:24429958..24432815,2	K562	blood:
6	chr6:24402229..24405454-chr6:24428896..24431433,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112293	Chromatin interaction
ENSG00000112294	Chromatin interaction
ENSG00000124532	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1742273	0.85[EUR][1000 genomes]
rs2273605	0.80[EUR][1000 genomes]
rs2487515	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2753913	0.85[EUR][1000 genomes]
rs2753915	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2753927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2793423	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2793424	0.84[EUR][1000 genomes]
rs2793425	0.86[EUR][1000 genomes]
rs2793426	0.86[EUR][1000 genomes]
rs2793427	0.86[EUR][1000 genomes]
rs35618643	0.85[ASN][1000 genomes]
rs3736798	0.94[ASN][1000 genomes]
rs3747768	0.85[ASN][1000 genomes]
rs6942189	0.89[EUR][1000 genomes]
rs7750377	0.94[ASN][1000 genomes]
rs793672	0.95[CHB][hapmap];0.84[EUR][1000 genomes]
rs793673	0.87[CHB][hapmap]
rs793681	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs793684	0.92[AFR][1000 genomes]
rs793686	0.92[AFR][1000 genomes]
rs793687	0.91[AFR][1000 genomes]
rs793688	0.96[LWK][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes]
rs793689	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs796985	0.91[CHB][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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs793683	ZNF192	cis	parietal	SCAN
rs793683	HIST1H2BC	cis	parietal	SCAN
rs793683	HIST1H2BG	cis	parietal	SCAN
rs793683	MRS2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24404600-24437400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:24410000-24430800	Strong transcription	Left Ventricle	heart
3	chr6:24412600-24430800	Strong transcription	Primary T cells from cord blood	blood
4	chr6:24417400-24451800	Strong transcription	Liver	Liver
5	chr6:24421200-24448800	Weak transcription	Gastric	stomach
6	chr6:24421200-24459600	Weak transcription	Spleen	Spleen
7	chr6:24421400-24434000	Weak transcription	Fetal Brain Male	brain
8	chr6:24421600-24432000	Weak transcription	Fetal Heart	heart
9	chr6:24422400-24431400	Weak transcription	Fetal Intestine Small	intestine
10	chr6:24422400-24437400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:24423400-24433600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr6:24423400-24437200	Weak transcription	Pancreas	Pancrea
13	chr6:24423400-24439400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr6:24423600-24437200	Weak transcription	Right Ventricle	heart
15	chr6:24423800-24432000	Weak transcription	NHEK	skin
16	chr6:24424000-24432200	Weak transcription	Small Intestine	intestine
17	chr6:24424000-24456600	Weak transcription	Ovary	ovary
18	chr6:24424400-24445800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr6:24425400-24432000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr6:24425400-24437200	Weak transcription	Brain Cingulate Gyrus	brain
21	chr6:24425400-24439600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr6:24426000-24431000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr6:24426000-24438800	Weak transcription	Brain Substantia Nigra	brain
24	chr6:24426200-24430600	Weak transcription	Esophagus	oesophagus
25	chr6:24426200-24431600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr6:24426200-24446000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr6:24426400-24431400	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr6:24426400-24432400	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr6:24426400-24441600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr6:24426400-24446000	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr6:24426600-24438800	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr6:24427000-24431600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr6:24427200-24433800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr6:24427400-24435000	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr6:24427600-24432400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr6:24427600-24433800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr6:24427600-24436600	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr6:24427600-24437600	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr6:24427600-24439200	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr6:24427600-24439400	Weak transcription	Fetal Thymus	thymus
41	chr6:24427600-24440000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr6:24427600-24440000	Weak transcription	Dnd41	blood
43	chr6:24427600-24441800	Weak transcription	Primary B cells from peripheral blood	blood
44	chr6:24427600-24445600	Weak transcription	Fetal Brain Female	brain
45	chr6:24427600-24456800	Weak transcription	Lung	lung
46	chr6:24427800-24431800	Weak transcription	Fetal Intestine Large	intestine
47	chr6:24427800-24435800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr6:24427800-24467000	Weak transcription	Brain Germinal Matrix	brain
49	chr6:24428200-24431200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr6:24428200-24432600	Weak transcription	GM12878-XiMat	blood

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