Variant report

Variant	rs929156
Chromosome Location	chr6:30139699-30139700
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:30134299..30136514-chr6:30137950..30139841,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000204610	Chromatin interaction

Extended variants
information (count: 126 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs1042338	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1076229	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13194768	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1419671	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1419672	0.88[EUR][1000 genomes]
rs1419673	0.82[EUR][1000 genomes]
rs1541324	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1573297	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1573298	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1573299	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17194607	0.82[ASN][1000 genomes]
rs2239530	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2285795	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2285796	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2508030	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2508031	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2517606	0.80[ASN][1000 genomes]
rs2517616	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2517653	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2517655	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2844775	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2857433	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2857435	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2857436	0.83[ASN][1000 genomes]
rs2857438	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2857439	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2857440	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2857458	0.83[ASN][1000 genomes]
rs3778622	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3815079	0.83[ASN][1000 genomes]
rs3815080	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3815082	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3815084	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3815085	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3815086	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3888580	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4392759	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4711211	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4713293	0.82[EUR][1000 genomes]
rs4959011	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4959012	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4959044	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs757259	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs757261	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs757262	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs757263	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs757264	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7843	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9261440	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9261442	0.82[EUR][1000 genomes]
rs9261443	0.89[EUR][1000 genomes]
rs9261444	0.82[EUR][1000 genomes]
rs9261445	0.82[EUR][1000 genomes]
rs9261446	0.82[EUR][1000 genomes]
rs9261448	0.82[EUR][1000 genomes]
rs9261449	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9261450	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9261451	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9261453	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9261454	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9261455	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9261456	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9261457	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9261458	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9261459	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9261461	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9261462	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9261463	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9261465	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9261466	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9261467	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9261468	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9261470	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9261471	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9261472	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9261473	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9261479	0.83[EUR][1000 genomes]
rs9261480	0.83[EUR][1000 genomes]
rs9261482	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9261483	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9261484	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9261485	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9261486	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9261488	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9261489	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9261490	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261491	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261492	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261493	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9261495	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9261496	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261497	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261498	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9261499	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9261500	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9261501	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261502	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261503	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9261504	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9261505	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9261507	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261508	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261509	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261511	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9261512	0.84[ASN][1000 genomes]
rs9261513	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9261514	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9261516	0.82[ASN][1000 genomes]
rs9261517	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9261518	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261519	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261521	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9261522	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9261523	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261524	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9261525	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261526	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9261527	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9261528	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9261529	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9261530	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9261531	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9261532	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9261533	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9261535	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs957765	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs929156	HIST1H2AM	cis	parietal	SCAN
rs929156	ZKSCAN3	cis	cerebellum	SCAN
rs929156	HIST1H2BN	cis	parietal	SCAN
rs929156	HIST1H2AI	cis	parietal	SCAN
rs929156	BTN2A1	cis	cerebellum	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30135600-30141200	Strong transcription	HepG2	liver
2	chr6:30138200-30140200	Strong transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:30139000-30152000	Weak transcription	Liver	Liver
4	chr6:30139400-30139800	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:30139400-30139800	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
6	chr6:30139400-30139800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr6:30139400-30139800	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
8	chr6:30139400-30139800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
9	chr6:30139400-30139800	Bivalent Enhancer	Fetal Intestine Large	intestine
10	chr6:30139400-30139800	Bivalent Enhancer	Fetal Intestine Small	intestine
11	chr6:30139400-30139800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
12	chr6:30139400-30139800	Flanking Active TSS	Right Ventricle	heart
13	chr6:30139400-30139800	Bivalent Enhancer	Stomach Mucosa	stomach
14	chr6:30139400-30139800	Bivalent Enhancer	NHDF-Ad	bronchial
15	chr6:30139400-30140000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
16	chr6:30139400-30140000	Bivalent Enhancer	Fetal Heart	heart
17	chr6:30139400-30140000	Bivalent Enhancer	Placenta	Placenta
18	chr6:30139400-30140000	Enhancers	Gastric	stomach
19	chr6:30139400-30140200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:30139400-30140200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr6:30139400-30140200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr6:30139400-30140200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
23	chr6:30139400-30140200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr6:30139400-30140200	Enhancers	Pancreas	Pancrea
25	chr6:30139400-30140400	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr6:30139400-30140400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
27	chr6:30139400-30140400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
28	chr6:30139400-30140400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
29	chr6:30139400-30140400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
30	chr6:30139400-30140400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
31	chr6:30139400-30140400	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
32	chr6:30139400-30140400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
33	chr6:30139400-30140400	Bivalent Enhancer	Esophagus	oesophagus
34	chr6:30139400-30140600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
35	chr6:30139400-30140800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
36	chr6:30139600-30139800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr6:30139600-30139800	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr6:30139600-30139800	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
39	chr6:30139600-30139800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr6:30139600-30139800	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
41	chr6:30139600-30139800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
42	chr6:30139600-30139800	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
43	chr6:30139600-30139800	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
44	chr6:30139600-30139800	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
45	chr6:30139600-30140000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
46	chr6:30139600-30140000	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
47	chr6:30139600-30140000	Bivalent Enhancer	Brain Cingulate Gyrus	brain
48	chr6:30139600-30140000	Bivalent Enhancer	Brain Hippocampus Middle	brain
49	chr6:30139600-30140000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
50	chr6:30139600-30140000	Weak transcription	Rectal Mucosa Donor 31	rectum

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