Variant report

Variant	rs200965
Chromosome Location	chr6:27866384-27866385
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	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	chr6:27866006-27866528	K562	blood:	n/a	n/a
4	POLR2A	chr6:27865300-27866561	K562	blood:	n/a	n/a
5	POLR2A	chr6:27866088-27867173	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr6:27856294-27871164	K562	blood:	n/a	n/a
7	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	chr6:27105394..27120060-chr6:27855994..27866393,42	K562	blood:
4	chr6:27094943..27118570-chr6:27854106..27868030,101	K562	blood:

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

Extended variants
information (count: 93 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1015075	0.85[JPT][hapmap]
rs12174918	0.82[ASN][1000 genomes]
rs16867962	1.00[CHB][hapmap]
rs169287	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs175597	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.89[ASN][1000 genomes]
rs17693877	1.00[CHB][hapmap]
rs183225	1.00[JPT][hapmap]
rs200466	1.00[JPT][hapmap]
rs200469	1.00[JPT][hapmap]
rs200473	1.00[JPT][hapmap]
rs200479	1.00[JPT][hapmap]
rs200481	0.80[ASN][1000 genomes]
rs200482	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs200483	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs200484	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs200485	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs200487	0.81[YRI][hapmap]
rs200488	0.89[ASN][1000 genomes]
rs200489	0.89[ASN][1000 genomes]
rs200490	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[ASN][1000 genomes]
rs200497	0.86[ASN][1000 genomes]
rs200498	0.84[ASN][1000 genomes]
rs200499	0.82[ASN][1000 genomes]
rs200501	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs200947	0.82[YRI][hapmap]
rs200948	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[ASN][1000 genomes]
rs200949	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs200950	0.93[ASN][1000 genomes]
rs200952	0.93[ASN][1000 genomes]
rs200953	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs200954	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[ASN][1000 genomes]
rs200955	0.88[YRI][hapmap]
rs200964	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs200966	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs200968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs200974	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs200976	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs200977	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs200979	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200980	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200981	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[ASN][1000 genomes]
rs200982	0.83[YRI][hapmap]
rs200983	0.89[ASN][1000 genomes]
rs200984	0.83[YRI][hapmap]
rs200989	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.89[ASN][1000 genomes]
rs200990	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[ASN][1000 genomes]
rs200992	0.87[ASN][1000 genomes]
rs200995	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs200996	0.89[ASN][1000 genomes]
rs201002	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[ASN][1000 genomes]
rs201005	0.88[YRI][hapmap]
rs2277104	0.86[ASN][1000 genomes]
rs2394001	0.82[ASN][1000 genomes]
rs2747054	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs34295134	0.89[ASN][1000 genomes]
rs36108923	0.89[ASN][1000 genomes]
rs370155	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs390764	0.87[ASN][1000 genomes]
rs401754	0.87[ASN][1000 genomes]
rs401763	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4713122	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4713124	0.82[ASN][1000 genomes]
rs4713127	0.95[ASN][1000 genomes]
rs483143	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs493161	0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs494887	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs557042	0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs56870390	0.89[ASN][1000 genomes]
rs59015666	0.82[ASN][1000 genomes]
rs666846	1.00[JPT][hapmap]
rs904142	0.85[JPT][hapmap]
rs9348779	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9357052	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9368531	0.87[ASN][1000 genomes]
rs9368534	0.86[ASN][1000 genomes]
rs9368535	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9368536	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9368537	0.85[JPT][hapmap]
rs9380018	0.80[ASN][1000 genomes]
rs9380026	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9380028	0.85[JPT][hapmap]
rs9380030	0.85[JPT][hapmap]
rs9393854	1.00[CHB][hapmap]
rs9393858	0.87[ASN][1000 genomes]
rs9393862	0.95[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs200965	Hs.158943	cis	multi-tissue	Pritchard
rs200965	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs200965	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs200965	AL022393.7	cis	Muscle Skeletal	GTEx
rs200965	OR2B8P	cis	Thyroid	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	chr6:27865000-27866400	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr6:27865200-27866400	Enhancers	GM12878-XiMat	blood
28	chr6:27865200-27869200	Weak transcription	Dnd41	blood
29	chr6:27865600-27867000	Enhancers	Placenta Amnion	Placenta Amnion
30	chr6:27865800-27867200	Enhancers	Placenta	Placenta
31	chr6:27865800-27869400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr6:27865800-27870000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr6:27866000-27866800	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr6:27866000-27870000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr6:27866200-27867000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr6:27866200-27869600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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