Variant report

Variant	rs200964
Chromosome Location	chr6:27866943-27866944
allele	C/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	BCLAF1	chr6:27856983-27867279	K562	blood:	n/a	chr6:27863647-27863660 chr6:27863652-27863661 chr6:27862695-27862704 chr6:27857910-27857919
2	POLR2A	chr6:27856821-27873085	K562	blood:	n/a	n/a
3	POLR2A	chr6:27866088-27867173	H1-hESC	embryonic stem cell:	n/a	n/a
4	CHD2	chr6:27866857-27867055	K562	blood:	n/a	n/a
5	POLR2A	chr6:27856294-27871164	K562	blood:	n/a	n/a
6	POLR2A	chr6:27856914-27866947	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:27518690..27520835-chr6:27865558..27867263,2	K562	blood:
2	chr13:92000008..92002125-chr6:27865373..27867459,2	K562	blood:
3	chr6:27094943..27118570-chr6:27854106..27868030,101	K562	blood:

Variant related genes	Relation type
RNU7-26P	TF binding region
ENSG00000198339	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000215417	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000265565	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs12174918	0.80[ASN][1000 genomes]
rs169287	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs175597	0.87[ASN][1000 genomes]
rs200481	0.83[ASN][1000 genomes]
rs200482	0.83[ASN][1000 genomes]
rs200483	0.80[ASN][1000 genomes]
rs200488	0.87[ASN][1000 genomes]
rs200489	0.87[ASN][1000 genomes]
rs200490	0.84[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs200497	0.84[ASN][1000 genomes]
rs200498	0.82[ASN][1000 genomes]
rs200499	0.80[ASN][1000 genomes]
rs200501	0.83[ASN][1000 genomes]
rs200948	0.91[ASN][1000 genomes]
rs200949	0.93[ASN][1000 genomes]
rs200950	0.91[ASN][1000 genomes]
rs200952	0.91[ASN][1000 genomes]
rs200953	0.91[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs200954	0.91[ASN][1000 genomes]
rs200965	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs200966	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200968	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs200973	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs200974	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs200975	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs200976	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200977	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs200979	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs200980	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs200981	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs200983	0.87[ASN][1000 genomes]
rs200989	0.87[ASN][1000 genomes]
rs200990	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs200992	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs200995	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs200996	0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs201002	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2277104	0.84[ASN][1000 genomes]
rs2394001	0.80[ASN][1000 genomes]
rs2747054	0.85[ASN][1000 genomes]
rs34295134	0.87[ASN][1000 genomes]
rs36108923	0.87[ASN][1000 genomes]
rs370155	0.80[ASN][1000 genomes]
rs390764	0.85[ASN][1000 genomes]
rs401754	0.85[ASN][1000 genomes]
rs401763	0.82[ASN][1000 genomes]
rs4713122	0.80[ASN][1000 genomes]
rs4713124	0.80[ASN][1000 genomes]
rs4713127	0.93[ASN][1000 genomes]
rs483143	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs493161	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs494887	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs557042	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs56870390	0.87[ASN][1000 genomes]
rs59015666	0.80[ASN][1000 genomes]
rs9348779	0.91[ASN][1000 genomes]
rs9357052	0.93[ASN][1000 genomes]
rs9368531	0.85[ASN][1000 genomes]
rs9368534	0.84[ASN][1000 genomes]
rs9368535	0.91[ASN][1000 genomes]
rs9368536	0.91[ASN][1000 genomes]
rs9380026	0.93[ASN][1000 genomes]
rs9393858	0.85[ASN][1000 genomes]
rs9393862	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432858	chr6:27719375-28011652	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	387 gene(s)	inside rSNPs	diseases
2	nsv1022173	chr6:27734824-27959408	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
3	nsv883512	chr6:27748631-27969004	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
4	nsv601208	chr6:27810626-27969004	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	237 gene(s)	inside rSNPs	diseases
5	nsv601209	chr6:27849676-27869321	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	194 gene(s)	inside rSNPs	diseases
6	nsv1022651	chr6:27864217-28017997	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs200964	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs200964	OR2B8P	cis	Thyroid	GTEx
rs200964	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs200964	AL022393.7	cis	Muscle Skeletal	GTEx

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27863800-27870000	Weak transcription	Primary T cells from cord blood	blood
2	chr6:27863800-27870000	Weak transcription	Adipose Nuclei	Adipose
3	chr6:27863800-27870400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr6:27864000-27869400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:27864000-27869400	Weak transcription	HMEC	breast
6	chr6:27864000-27869600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr6:27864000-27870000	Weak transcription	NHEK	skin
8	chr6:27864000-27870200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr6:27864200-27867000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr6:27864200-27867400	Transcr. at gene 5' and 3'	K562	blood
11	chr6:27864200-27870000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr6:27864200-27870400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:27864400-27869600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr6:27864400-27870000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr6:27864400-27870000	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr6:27864400-27870000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr6:27864400-27870000	Weak transcription	Fetal Intestine Small	intestine
18	chr6:27864600-27867400	Enhancers	Hela-S3	cervix
19	chr6:27864600-27867800	Weak transcription	HepG2	liver
20	chr6:27864600-27869400	Weak transcription	A549	lung
21	chr6:27864600-27870000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr6:27864600-27870000	Weak transcription	Primary hematopoietic stem cells	blood
23	chr6:27864600-27870000	Weak transcription	Fetal Kidney	kidney
24	chr6:27864600-27870000	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr6:27864800-27869600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr6:27865200-27869200	Weak transcription	Dnd41	blood
27	chr6:27865600-27867000	Enhancers	Placenta Amnion	Placenta Amnion
28	chr6:27865800-27867200	Enhancers	Placenta	Placenta
29	chr6:27865800-27869400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr6:27865800-27870000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr6:27866000-27870000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr6:27866200-27867000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr6:27866200-27869600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr6:27866400-27870000	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr6:27866600-27867000	Enhancers	GM12878-XiMat	blood
36	chr6:27866800-27867200	Weak transcription	HUES48 Cell Line	embryonic stem cell

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