Variant report

Variant	rs2852500
Chromosome Location	chr6:101841721-101841722
allele	A/C
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	SMARCB1	chr6:101840574-101842241	Hela-S3	cervix:	n/a	n/a
2	RAD21	chr6:101841238-101841819	MCF-7	breast:	n/a	chr6:101841726-101841739
3	RAD21	chr6:101841219-101841769	H1-hESC	embryonic stem cell:	n/a	chr6:101841726-101841739
4	SMC3	chr6:101841114-101841979	Hela-S3	cervix:	n/a	chr6:101841305-101841315 chr6:101841870-101841880
5	GATA2	chr6:101840430-101842060	SH-SY5Y	brain:	n/a	n/a
6	POLR2A	chr6:101841533-101841787	ProgFib	skin:	n/a	n/a
7	POLR2A	chr6:101841237-101842097	SK-N-MC	brain:	n/a	n/a
8	CREB1	chr6:101841090-101841852	H1-hESC	embryonic stem cell:	n/a	n/a
9	MAZ	chr6:101841329-101842049	Hela-S3	cervix:	n/a	n/a
10	MXI1	chr6:101840627-101843576	SK-N-SH	brain:	n/a	n/a
11	RAD21	chr6:101841175-101841854	H1-hESC	embryonic stem cell:	n/a	chr6:101841726-101841739
12	POLR2A	chr6:101841147-101842236	H1-neurons	neurons:	n/a	n/a
13	SIN3A	chr6:101840804-101842069	H1-hESC	embryonic stem cell:	n/a	chr6:101841312-101841323
14	CTCF	chr6:101841192-101842010	IMR90	lung:	n/a	n/a
15	POLR2A	chr6:101841300-101842132	MCF-7	breast:	n/a	n/a
16	RAD21	chr6:101840790-101842290	IMR90	lung:	n/a	chr6:101841726-101841739
17	POLR2A	chr6:101841226-101842143	MCF-7	breast:	n/a	n/a
18	TCF7L2	chr6:101841184-101842078	HCT-116	colon:	n/a	n/a
19	MAX	chr6:101841210-101841727	ECC-1	luminal epithelium:	n/a	n/a
20	CTCF	chr6:101841720-101841870	AG04449	skin:	n/a	n/a
21	POLR2A	chr6:101841227-101842272	H1-neurons	neurons:	n/a	n/a
22	CTBP2	chr6:101840400-101842190	H1-hESC	embryonic stem cell:	n/a	n/a
23	CHD2	chr6:101841478-101842202	Hela-S3	cervix:	n/a	chr6:101841478-101841485
24	POLR2A	chr6:101841076-101842187	IMR90	lung:	n/a	n/a
25	MAX	chr6:101841246-101841761	A549	lung:	n/a	n/a
26	POLR2A	chr6:101841250-101842026	Gliobla	brain:	n/a	n/a
27	POLR2A	chr6:101841466-101841737	Hela-S3	cervix:	n/a	n/a
28	MAZ	chr6:101840380-101842435	IMR90	lung:	n/a	chr6:101841145-101841154

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:39717339..39717957-chr6:101841486..101842139,2	MCF-7	breast:
2	chr6:101839704..101841744-chr6:101842658..101845506,3	K562	blood:

Variant related genes	Relation type
GRIK2	TF binding region

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1160258	0.83[ASN][1000 genomes]
rs17658674	0.83[ASN][1000 genomes]
rs1948050	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2518173	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2518319	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2579929	0.97[EUR][1000 genomes]
rs2629982	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2787573	0.97[EUR][1000 genomes]
rs283186	0.86[ASN][1000 genomes]
rs2852497	0.90[EUR][1000 genomes]
rs2852502	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2852503	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2852504	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2852505	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2852506	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2852507	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2852509	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2852510	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2852511	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2852512	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2852513	0.97[EUR][1000 genomes]
rs2852514	0.97[EUR][1000 genomes]
rs471631	1.00[ASN][1000 genomes]
rs473846	1.00[ASN][1000 genomes]
rs480221	1.00[ASN][1000 genomes]
rs484819	1.00[ASN][1000 genomes]
rs489458	1.00[ASN][1000 genomes]
rs493123	1.00[ASN][1000 genomes]
rs496596	0.84[EUR][1000 genomes]
rs500305	1.00[ASN][1000 genomes]
rs503387	0.90[EUR][1000 genomes]
rs504406	1.00[ASN][1000 genomes]
rs504408	1.00[ASN][1000 genomes]
rs528879	1.00[ASN][1000 genomes]
rs542820	1.00[ASN][1000 genomes]
rs542923	1.00[ASN][1000 genomes]
rs546327	1.00[ASN][1000 genomes]
rs566507	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs570556	0.84[EUR][1000 genomes]
rs577503	1.00[ASN][1000 genomes]
rs579069	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs584655	1.00[ASN][1000 genomes]
rs594870	1.00[ASN][1000 genomes]
rs600842	1.00[ASN][1000 genomes]
rs608847	1.00[ASN][1000 genomes]
rs632956	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs636796	1.00[ASN][1000 genomes]
rs638255	1.00[ASN][1000 genomes]
rs661064	0.90[EUR][1000 genomes]
rs662360	0.89[EUR][1000 genomes]
rs662916	1.00[ASN][1000 genomes]
rs668267	1.00[ASN][1000 genomes]
rs675259	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs683149	1.00[ASN][1000 genomes]
rs684160	1.00[ASN][1000 genomes]
rs685002	1.00[ASN][1000 genomes]
rs687497	0.89[EUR][1000 genomes]
rs697440	1.00[ASN][1000 genomes]
rs697441	1.00[ASN][1000 genomes]
rs808952	1.00[ASN][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	nsv1020400	chr6:101172705-101981665	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv538390	chr6:101172705-101981665	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:101839600-101842200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr6:101839600-101842200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
3	chr6:101839600-101842200	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr6:101839600-101842400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
5	chr6:101839600-101842400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
6	chr6:101839800-101842200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
7	chr6:101840000-101842200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr6:101840000-101842200	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr6:101840000-101842200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:101840000-101842400	Active TSS	H9 Cell Line	embryonic stem cell
11	chr6:101840000-101842400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
12	chr6:101840000-101843600	Active TSS	Right Atrium	heart
13	chr6:101840200-101842000	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr6:101840200-101842200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr6:101840200-101842400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
16	chr6:101840400-101842200	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
17	chr6:101840400-101842200	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
18	chr6:101840400-101842400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:101840400-101843200	Bivalent/Poised TSS	Fetal Kidney	kidney
20	chr6:101840600-101842000	Bivalent/Poised TSS	NHDF-Ad	bronchial
21	chr6:101840600-101842200	Active TSS	Right Ventricle	heart
22	chr6:101840800-101842200	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
23	chr6:101840800-101842200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
24	chr6:101841000-101842000	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:101841000-101842000	Bivalent/Poised TSS	A549	lung
26	chr6:101841000-101842200	Bivalent Enhancer	Primary hematopoietic stem cells	blood
27	chr6:101841000-101842200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr6:101841000-101842200	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
29	chr6:101841000-101842200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
30	chr6:101841000-101842800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr6:101841200-101842000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr6:101841200-101842000	Active TSS	NHLF	lung
33	chr6:101841200-101842200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:101841200-101842200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
35	chr6:101841200-101842200	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
36	chr6:101841200-101842200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
37	chr6:101841200-101842200	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
38	chr6:101841200-101842200	Bivalent/Poised TSS	Osteobl	bone
39	chr6:101841200-101842600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr6:101841200-101842800	Bivalent/Poised TSS	Fetal Brain Female	brain
41	chr6:101841400-101841800	Bivalent/Poised TSS	Breast Myoepithelial Primary Cells	Breast
42	chr6:101841400-101841800	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr6:101841400-101841800	Active TSS	Brain Inferior Temporal Lobe	brain
44	chr6:101841400-101841800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr6:101841400-101841800	Bivalent/Poised TSS	Esophagus	oesophagus
46	chr6:101841400-101841800	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
47	chr6:101841400-101841800	Bivalent Enhancer	Placenta	Placenta
48	chr6:101841400-101841800	Bivalent/Poised TSS	Fetal Stomach	stomach
49	chr6:101841400-101841800	Bivalent/Poised TSS	HMEC	breast
50	chr6:101841400-101842000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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