Variant report

Variant	rs6932378
Chromosome Location	chr6:5851500-5851501
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	chr6:5851316-5852032	H1-neurons	neurons:	n/a	n/a
2	ATF2	chr6:5850961-5852209	H1-hESC	embryonic stem cell:	n/a	n/a
3	TCF12	chr6:5850981-5851561	H1-hESC	embryonic stem cell:	n/a	chr6:5851365-5851372
4	EP300	chr6:5851061-5851519	H1-hESC	embryonic stem cell:	n/a	n/a
5	TEAD4	chr6:5851052-5851858	H1-hESC	embryonic stem cell:	n/a	n/a
6	YY1	chr6:5851135-5851802	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr6:5851125-5851516	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr6:5851459-5851941	GM12892	blood:	n/a	n/a
9	SIN3A	chr6:5851002-5851500	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr6:5850657-5852284	H1-hESC	embryonic stem cell:	n/a	n/a
11	ATF2	chr6:5851393-5851850	GM12878	blood:	n/a	n/a
12	POLR2A	chr6:5850727-5852069	H1-hESC	embryonic stem cell:	n/a	n/a
13	MAX	chr6:5851064-5852213	H1-hESC	embryonic stem cell:	n/a	chr6:5851945-5851952 chr6:5851942-5851953 chr6:5851944-5851953 chr6:5851375-5851385
14	CTBP2	chr6:5851148-5851686	H1-hESC	embryonic stem cell:	n/a	n/a
15	TBP	chr6:5851125-5851850	H1-hESC	embryonic stem cell:	n/a	n/a
16	ATF2	chr6:5851385-5851858	GM12878	blood:	n/a	n/a
17	TEAD4	chr6:5850918-5851551	H1-hESC	embryonic stem cell:	n/a	n/a
18	RAD21	chr6:5850973-5851539	H1-hESC	embryonic stem cell:	n/a	chr6:5851059-5851072 chr6:5851018-5851027
19	POLR2A	chr6:5851030-5852070	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr6:5851073-5851552	H1-hESC	embryonic stem cell:	n/a	n/a
21	E2F6	chr6:5851144-5852254	H1-hESC	embryonic stem cell:	n/a	n/a
22	SP1	chr6:5851001-5851570	H1-hESC	embryonic stem cell:	n/a	chr6:5851371-5851385 chr6:5851374-5851386 chr6:5851374-5851386
23	ATF2	chr6:5850966-5852068	H1-hESC	embryonic stem cell:	n/a	n/a
24	TAF1	chr6:5851126-5851500	H1-hESC	embryonic stem cell:	n/a	n/a
25	TAF1	chr6:5851057-5852124	H1-hESC	embryonic stem cell:	n/a	n/a
26	SP1	chr6:5850982-5851879	H1-hESC	embryonic stem cell:	n/a	chr6:5851371-5851385 chr6:5851374-5851386 chr6:5851598-5851619 chr6:5851374-5851386
27	NFYA	chr6:5851407-5851685	K562	blood:	n/a	chr6:5851643-5851658 chr6:5851644-5851658 chr6:5851646-5851656 chr6:5851643-5851658
28	CEBPB	chr6:5851181-5851786	H1-hESC	embryonic stem cell:	n/a	n/a
29	CHD2	chr6:5851127-5851863	H1-hESC	embryonic stem cell:	n/a	chr6:5851693-5851703
30	YY1	chr6:5851140-5852544	H1-hESC	embryonic stem cell:	n/a	n/a
31	JUN	chr6:5851270-5851705	H1-hESC	embryonic stem cell:	n/a	n/a
32	TCF12	chr6:5851152-5851535	H1-hESC	embryonic stem cell:	n/a	chr6:5851365-5851372
33	JUND	chr6:5850837-5851802	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
ENSG00000233064	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs13191588	0.84[AMR][1000 genomes]
rs17145829	0.90[EUR][1000 genomes]
rs2004508	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35636471	0.81[AMR][1000 genomes]
rs9378988	0.81[AMR][1000 genomes]
rs9405875	0.82[AMR][1000 genomes]
rs9405876	0.85[AMR][1000 genomes]
rs9502354	0.84[AMR][1000 genomes]
rs9504546	0.82[AMR][1000 genomes]

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	nsv5183	chr6:5821731-5866796	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5850800-5852200	Active TSS	Brain Cingulate Gyrus	brain
2	chr6:5850800-5852200	Active TSS	Fetal Brain Female	brain
3	chr6:5850800-5852400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr6:5851000-5851600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:5851000-5851600	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
6	chr6:5851000-5851600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
7	chr6:5851000-5851800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:5851000-5851800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:5851000-5851800	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr6:5851000-5852000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:5851000-5852000	Active TSS	Brain Hippocampus Middle	brain
12	chr6:5851000-5852000	Bivalent/Poised TSS	Fetal Intestine Small	intestine
13	chr6:5851000-5852000	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr6:5851000-5852000	Active TSS	Right Atrium	heart
15	chr6:5851000-5852000	Active TSS	Right Ventricle	heart
16	chr6:5851000-5852000	Enhancers	Spleen	Spleen
17	chr6:5851000-5852200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr6:5851000-5852200	Active TSS	Primary T cells from cord blood	blood
19	chr6:5851000-5852200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr6:5851000-5852200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
21	chr6:5851000-5852200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr6:5851000-5852200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr6:5851000-5852200	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr6:5851000-5852200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr6:5851000-5852200	Active TSS	Brain Substantia Nigra	brain
26	chr6:5851000-5852400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
27	chr6:5851000-5852400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
28	chr6:5851000-5852400	Active TSS	Brain Anterior Caudate	brain
29	chr6:5851200-5851600	Active TSS	H1 Cell Line	embryonic stem cell
30	chr6:5851200-5851600	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr6:5851200-5851600	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
32	chr6:5851200-5851600	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
33	chr6:5851200-5851600	Active TSS	Colonic Mucosa	Colon
34	chr6:5851200-5851600	Bivalent Enhancer	Fetal Heart	heart
35	chr6:5851200-5851600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
36	chr6:5851200-5851600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
37	chr6:5851200-5851600	Flanking Active TSS	Fetal Thymus	thymus
38	chr6:5851200-5851600	Active TSS	Psoas Muscle	Psoas
39	chr6:5851200-5851600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
40	chr6:5851200-5851600	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
41	chr6:5851200-5851600	Bivalent/Poised TSS	Thymus	Thymus
42	chr6:5851200-5851800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
43	chr6:5851200-5851800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
44	chr6:5851200-5851800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr6:5851200-5851800	Active TSS	Fetal Brain Male	brain
46	chr6:5851200-5851800	Active TSS	Gastric	stomach
47	chr6:5851200-5851800	Active TSS	Small Intestine	intestine
48	chr6:5851200-5852000	Flanking Active TSS	Primary hematopoietic stem cells	blood
49	chr6:5851200-5852000	Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr6:5851200-5852000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain

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