Variant report

Variant	rs200950
Chromosome Location	chr6:27835772-27835773
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:27831639-27835944	MCF-7	breast:	n/a	n/a
2	TAF7	chr6:27832651-27836396	H1-hESC	embryonic stem cell:	n/a	n/a
3	MYC	chr6:27833855-27836057	NB4	blood:	n/a	n/a
4	SIN3AK20	chr6:27832583-27835816	MCF-7	breast:	n/a	n/a
5	CEBPB	chr6:27832652-27835822	GM12878	blood:	n/a	chr6:27835599-27835610
6	RELA	chr6:27832746-27835808	GM10847	blood:	n/a	n/a
7	MXI1	chr6:27831650-27836500	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr6:27832456-27836599	H1-hESC	embryonic stem cell:	n/a	n/a
9	TCF7L2	chr6:27834813-27835816	PANC-1	pancreas:	n/a	n/a
10	POLR2A	chr6:27835709-27836049	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:116915588..116917427-chr6:27834235..27836471,2	MCF-7	breast:
2	chr6:27098237..27102845-chr6:27835694..27840254,5	MCF-7	breast:
3	chr1:11967132..11968839-chr6:27832941..27835901,2	MCF-7	breast:
4	chr6:26154866..26157028-chr6:27832028..27836151,3	MCF-7	breast:
5	chr6:26249129..26252003-chr6:27832611..27836378,6	MCF-7	breast:
6	chr17:56735249..56737009-chr6:27834194..27835800,2	MCF-7	breast:
7	chr6:26156108..26158898-chr6:27832756..27836611,3	MCF-7	breast:
8	chr6:27113081..27116777-chr6:27832860..27836046,4	K562	blood:
9	chr6:26033297..26035200-chr6:27833856..27836117,3	MCF-7	breast:
10	chr6:27105570..27109142-chr6:27832678..27836176,3	K562	blood:
11	chr6:27834624..27836124-chr7:99722099..99724739,2	MCF-7	breast:
12	chr6:26044265..26046503-chr6:27834017..27836277,2	MCF-7	breast:
13	chr6:26019660..26022685-chr6:27833901..27836758,3	MCF-7	breast:
14	chr6:27833103..27835859-chr6:28582647..28584529,2	K562	blood:
15	chr6:26123459..26125455-chr6:27834569..27837416,2	MCF-7	breast:
16	chr6:27113591..27118417-chr6:27832860..27835856,7	K562	blood:
17	chr1:149855909..149858308-chr6:27833822..27835971,2	MCF-7	breast:
18	chr6:26123458..26125812-chr6:27833699..27835902,2	K562	blood:
19	chr16:4663445..4665916-chr6:27834145..27836986,3	MCF-7	breast:
20	chr1:16840036..16842043-chr6:27834742..27837032,2	MCF-7	breast:
21	chr6:27113113..27117592-chr6:27831181..27837403,7	MCF-7	breast:

No data

Variant related genes	Relation type
HIST1H1B	TF binding region
HIST1H2BPS2	TF binding region
ENSG00000256316	Chromatin interaction
ENSG00000168298	Chromatin interaction
ENSG00000196176	Chromatin interaction
ENSG00000199347	Chromatin interaction
ENSG00000196532	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000180596	Chromatin interaction
ENSG00000206652	Chromatin interaction
ENSG00000261135	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000163399	Chromatin interaction
ENSG00000153443	Chromatin interaction
ENSG00000197459	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000137259	Chromatin interaction
ENSG00000198366	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000180573	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000232040	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000214309	Chromatin interaction
ENSG00000198339	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs12174918	0.89[ASN][1000 genomes]
rs13194781	0.90[EUR][1000 genomes]
rs13195728	0.86[EUR][1000 genomes]
rs13199649	0.88[EUR][1000 genomes]
rs13199772	0.90[EUR][1000 genomes]
rs13199906	0.90[EUR][1000 genomes]
rs13212651	0.90[EUR][1000 genomes]
rs13216117	0.86[EUR][1000 genomes]
rs13218875	0.81[EUR][1000 genomes]
rs169287	0.91[ASN][1000 genomes]
rs175597	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17695758	0.90[EUR][1000 genomes]
rs17751184	0.86[EUR][1000 genomes]
rs17763089	0.90[EUR][1000 genomes]
rs183225	0.81[ASN][1000 genomes]
rs188015	0.84[EUR][1000 genomes]
rs200466	0.81[ASN][1000 genomes]
rs200471	0.81[ASN][1000 genomes]
rs200473	0.81[ASN][1000 genomes]
rs200478	0.81[ASN][1000 genomes]
rs200479	0.81[ASN][1000 genomes]
rs200481	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs200482	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs200483	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs200484	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs200485	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs200488	0.89[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs200489	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs200490	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs200493	0.92[EUR][1000 genomes]
rs200497	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs200498	0.91[ASN][1000 genomes]
rs200499	0.89[ASN][1000 genomes]
rs200501	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs200948	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200949	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs200952	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200953	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs200954	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200964	0.91[ASN][1000 genomes]
rs200965	0.93[ASN][1000 genomes]
rs200966	0.91[ASN][1000 genomes]
rs200968	0.93[ASN][1000 genomes]
rs200973	0.91[ASN][1000 genomes]
rs200974	0.93[ASN][1000 genomes]
rs200975	0.84[ASN][1000 genomes]
rs200976	0.91[ASN][1000 genomes]
rs200977	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs200979	0.93[ASN][1000 genomes]
rs200980	0.93[ASN][1000 genomes]
rs200981	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs200983	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs200989	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs200990	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs200992	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs200995	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs200996	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs201002	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2277104	0.93[ASN][1000 genomes]
rs2394001	0.89[ASN][1000 genomes]
rs2747054	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28360499	0.85[EUR][1000 genomes]
rs34194357	0.90[EUR][1000 genomes]
rs34295134	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34706883	0.86[EUR][1000 genomes]
rs34718920	0.86[EUR][1000 genomes]
rs34788973	0.86[EUR][1000 genomes]
rs35819751	0.90[EUR][1000 genomes]
rs36101351	0.86[EUR][1000 genomes]
rs36108923	0.95[ASN][1000 genomes]
rs36116761	0.90[EUR][1000 genomes]
rs370155	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs390764	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs401754	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs401763	0.91[ASN][1000 genomes]
rs45509595	0.90[EUR][1000 genomes]
rs4713122	0.89[ASN][1000 genomes]
rs4713124	0.89[ASN][1000 genomes]
rs4713127	0.98[ASN][1000 genomes]
rs483143	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs493161	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs494887	0.93[ASN][1000 genomes]
rs557042	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56870390	0.95[ASN][1000 genomes]
rs59015666	0.89[ASN][1000 genomes]
rs61742093	0.86[EUR][1000 genomes]
rs666846	0.81[ASN][1000 genomes]
rs66868086	0.90[EUR][1000 genomes]
rs67040724	0.86[EUR][1000 genomes]
rs67101035	0.86[EUR][1000 genomes]
rs71559050	0.86[EUR][1000 genomes]
rs71559054	0.86[EUR][1000 genomes]
rs9348779	1.00[ASN][1000 genomes]
rs9357052	0.98[ASN][1000 genomes]
rs9368531	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9368534	0.93[ASN][1000 genomes]
rs9368535	1.00[ASN][1000 genomes]
rs9368536	1.00[ASN][1000 genomes]
rs9380018	0.87[ASN][1000 genomes]
rs9380026	0.98[ASN][1000 genomes]
rs9393858	0.93[ASN][1000 genomes]
rs9393862	0.98[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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs200950	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs200950	ZFP57	Cis_chr	lymphoblastoid	RTeQTL
rs200950	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27830800-27835800	Active TSS	K562	blood
2	chr6:27831200-27835800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr6:27831200-27835800	Active TSS	H9 Cell Line	embryonic stem cell
4	chr6:27831600-27835800	Active TSS	Fetal Kidney	kidney
5	chr6:27831800-27835800	Active TSS	Aorta	Aorta
6	chr6:27832200-27836000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr6:27832800-27835800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:27832800-27835800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:27833000-27835800	Active TSS	H1 Cell Line	embryonic stem cell
10	chr6:27833000-27835800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr6:27833200-27835800	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr6:27833200-27836000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr6:27833200-27836200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:27833400-27836000	Flanking Active TSS	Primary T cells from cord blood	blood
15	chr6:27833400-27836000	Flanking Active TSS	Primary hematopoietic stem cells	blood
16	chr6:27833400-27836000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr6:27833800-27835800	Flanking Active TSS	HMEC	breast
18	chr6:27834000-27836000	Flanking Active TSS	NHEK	skin
19	chr6:27834200-27835800	Active TSS	Placenta Amnion	Placenta Amnion
20	chr6:27834400-27835800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
21	chr6:27834600-27835800	Active TSS	Thymus	Thymus
22	chr6:27834800-27835800	Bivalent/Poised TSS	Fetal Brain Female	brain
23	chr6:27834800-27835800	Active TSS	NHDF-Ad	bronchial
24	chr6:27835000-27835800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr6:27835000-27835800	Active TSS	Fetal Stomach	stomach
26	chr6:27835000-27836000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr6:27835000-27836000	Active TSS	Fetal Intestine Large	intestine
28	chr6:27835200-27835800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr6:27835200-27835800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr6:27835200-27835800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:27835200-27835800	Active TSS	Fetal Brain Male	brain
32	chr6:27835200-27835800	Active TSS	Rectal Mucosa Donor 31	rectum
33	chr6:27835200-27835800	Active TSS	Osteobl	bone
34	chr6:27835200-27836000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr6:27835200-27836000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr6:27835200-27838200	Weak transcription	Lung	lung
37	chr6:27835400-27835800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr6:27835400-27835800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr6:27835400-27835800	Enhancers	Liver	Liver
40	chr6:27835400-27835800	Bivalent Enhancer	Brain Angular Gyrus	brain
41	chr6:27835400-27835800	Active TSS	Fetal Heart	heart
42	chr6:27835400-27835800	Active TSS	Fetal Muscle Trunk	muscle
43	chr6:27835400-27835800	Active TSS	Fetal Muscle Leg	muscle
44	chr6:27835400-27835800	Active TSS	Rectal Mucosa Donor 29	rectum
45	chr6:27835400-27835800	Active TSS	Right Atrium	heart
46	chr6:27835400-27835800	Weak transcription	A549	lung
47	chr6:27835400-27835800	Flanking Active TSS	HUVEC	blood vessel
48	chr6:27835400-27836000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr6:27835400-27836000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
50	chr6:27835400-27836000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood

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