Variant report

Variant	rs200974
Chromosome Location	chr6:27855845-27855846
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:57917479..57925634-chr6:27855402..27862109,9	MCF-7	breast:
2	chr17:59482267..59483832-chr6:27855206..27857614,2	MCF-7	breast:
3	chr6:27096288..27105112-chr6:27855525..27865082,32	K562	blood:
4	chr6:27094943..27118570-chr6:27854106..27868030,101	K562	blood:

Variant related genes	Relation type
ENSG00000124635	Chromatin interaction
ENSG00000199004	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000201524	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000198339	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1015075	0.82[JPT][hapmap]
rs12174918	0.82[ASN][1000 genomes]
rs16867962	1.00[CHB][hapmap]
rs169287	0.91[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]
rs200488	0.89[ASN][1000 genomes]
rs200489	0.89[ASN][1000 genomes]
rs200490	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[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]
rs200948	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[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];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs200954	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[ASN][1000 genomes]
rs200964	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs200965	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]
rs200966	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs200968	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200973	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs200975	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs200976	0.85[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];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs200979	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200980	0.96[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];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs200983	0.89[ASN][1000 genomes]
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];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs200992	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs200995	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs200996	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs201002	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
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	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs494887	1.00[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	0.82[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	0.82[JPT][hapmap]
rs9380018	0.80[ASN][1000 genomes]
rs9380026	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9380028	0.82[JPT][hapmap]
rs9380030	0.82[JPT][hapmap]
rs9393845	0.88[CHB][hapmap]
rs9393854	1.00[CHB][hapmap]
rs9393858	0.87[ASN][1000 genomes]
rs9393862	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	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
3	nsv1017440	chr6:27734824-27864277	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	370 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs200974	Hs.158943	cis	multi-tissue	Pritchard
rs200974	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs200974	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs200974	AL022393.7	cis	Muscle Skeletal	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27842200-27857000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr6:27848200-27857000	Weak transcription	Thymus	Thymus
3	chr6:27850600-27857200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:27851200-27857400	Weak transcription	Placenta	Placenta
5	chr6:27855200-27856600	Enhancers	H1 Cell Line	embryonic stem cell
6	chr6:27855400-27856000	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr6:27855400-27856600	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr6:27855400-27857200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr6:27855600-27856000	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr6:27855600-27857000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:27855600-27857600	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr6:27855800-27856000	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr6:27855800-27856000	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr6:27855800-27856200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr6:27855800-27856400	Enhancers	H9 Cell Line	embryonic stem cell
16	chr6:27855800-27856400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr6:27855800-27856800	Enhancers	K562	blood
18	chr6:27855800-27857000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr6:27855800-27857000	Enhancers	Dnd41	blood
20	chr6:27855800-27857000	Enhancers	HepG2	liver
21	chr6:27855800-27857200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr6:27855800-27857200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr6:27855800-27857200	Enhancers	GM12878-XiMat	blood
24	chr6:27855800-27857400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr6:27855800-27857400	Enhancers	Fetal Thymus	thymus
26	chr6:27855800-27857800	Enhancers	Monocytes-CD14+_RO01746	blood

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