Variant report

Variant	rs2021719
Chromosome Location	chr6:30449482-30449483
allele	C/T
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	MAZ	chr6:30449478-30450378	IMR90	lung:	n/a	chr6:30450282-30450291
2	CTCF	chr6:30449480-30449630	SK-N-SH_RA	brain:	n/a	n/a
3	CTCF	chr6:30448729-30450259	SK-N-SH	brain:	n/a	chr6:30449066-30449082 chr6:30449226-30449235 chr6:30449067-30449080 chr6:30449344-30449352
4	CTCF	chr6:30449380-30449530	HCPEpiC	choroid plexus:	n/a	n/a
5	CTCF	chr6:30449440-30449710	HVMF	connective:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:30447797..30449612-chr6:30512660..30515323,2	MCF-7	breast:
2	chr6:30448465..30450230-chr6:30522710..30525074,2	K562	blood:
3	chr6:30447631..30450065-chr6:30691817..30695001,3	K562	blood:
4	chr6:30422351..30425241-chr6:30448232..30450888,2	MCF-7	breast:
5	chr6:30449301..30451388-chr6:30582216..30584322,2	K562	blood:
6	chr6:30446384..30451689-chr6:30578094..30585004,12	MCF-7	breast:
7	chr6:30448715..30451618-chr6:30508372..30511107,3	MCF-7	breast:
8	chr6:30448170..30453321-chr6:30582822..30586539,6	K562	blood:
9	chr6:30449369..30451271-chr6:30688942..30690860,2	MCF-7	breast:
10	chr6:30447949..30451648-chr6:30569801..30572499,4	MCF-7	breast:

Variant related genes	Relation type
RANP1	TF binding region
ENSG00000204568	Chromatin interaction
ENSG00000204569	Chromatin interaction
ENSG00000222894	Chromatin interaction
ENSG00000204590	Chromatin interaction
ENSG00000196230	Chromatin interaction
ENSG00000204576	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs2021720	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2105960	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2524192	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4711220	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6921669	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7747873	0.88[ASN][1000 genomes]
rs7761210	0.80[AMR][1000 genomes]
rs7764934	0.88[ASN][1000 genomes]
rs7775268	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9295898	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9295899	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9380180	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025667	chr6:30292845-30638066	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	825 gene(s)	inside rSNPs	diseases
2	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
4	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
5	nsv884069	chr6:30430875-30451474	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
6	nsv884070	chr6:30430875-30472772	Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
7	nsv884076	chr6:30434566-30483919	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
8	nsv884077	chr6:30434900-30512163	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
9	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	967 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2021719	GRM4	cis	parietal	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30447800-30450200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
2	chr6:30448000-30449800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
3	chr6:30448000-30450000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
4	chr6:30448000-30450200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
5	chr6:30448000-30450200	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
6	chr6:30448000-30450200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr6:30448200-30449600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
8	chr6:30448200-30450000	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:30448200-30450000	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
10	chr6:30448200-30450000	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
11	chr6:30448200-30450000	Bivalent Enhancer	Duodenum Mucosa	Duodenum
12	chr6:30448200-30450000	Bivalent Enhancer	Fetal Thymus	thymus
13	chr6:30448200-30450000	Bivalent Enhancer	GM12878-XiMat	blood
14	chr6:30448200-30450200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
15	chr6:30448200-30450400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
16	chr6:30448400-30449600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
17	chr6:30448400-30449800	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
18	chr6:30448400-30449800	Bivalent Enhancer	HUVEC	blood vessel
19	chr6:30448400-30450000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
20	chr6:30448400-30450000	Bivalent Enhancer	Primary B cells from cord blood	blood
21	chr6:30448400-30450000	Enhancers	Spleen	Spleen
22	chr6:30448400-30450000	Bivalent Enhancer	HMEC	breast
23	chr6:30448400-30450400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
24	chr6:30448600-30449600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr6:30448600-30449600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr6:30448600-30449800	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr6:30448600-30450000	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
28	chr6:30448800-30449600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
29	chr6:30448800-30449600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
30	chr6:30448800-30449800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
31	chr6:30448800-30450000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
32	chr6:30448800-30450000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr6:30448800-30450000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
34	chr6:30448800-30450200	Bivalent Enhancer	Fetal Stomach	stomach
35	chr6:30449000-30449600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr6:30449000-30449600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr6:30449000-30450000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
38	chr6:30449000-30450000	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr6:30449000-30450000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
40	chr6:30449000-30450000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
41	chr6:30449000-30450000	Flanking Bivalent TSS/Enh	HepG2	liver
42	chr6:30449000-30450200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
43	chr6:30449000-30450200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr6:30449200-30449600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
45	chr6:30449200-30449600	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr6:30449200-30449600	Bivalent Enhancer	NHEK	skin
47	chr6:30449200-30449800	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
48	chr6:30449200-30450000	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr6:30449200-30450000	Enhancers	Liver	Liver
50	chr6:30449200-30450000	Bivalent Enhancer	Fetal Muscle Leg	muscle

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