Variant report

Variant	rs200971
Chromosome Location	chr6:27858904-27858905
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:100)
CpG islands
(count:0)
Chromatin interactive
region (count:48)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:100 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:27857265-27863609	GM12891	blood:	n/a	n/a
2	TCF7L2	chr6:27857697-27859049	HCT-116	colon:	n/a	n/a
3	POLR2A	chr6:27857297-27858919	GM19099	blood:	n/a	n/a
4	POLR2A	chr6:27856971-27863786	K562	blood:	n/a	n/a
5	BCLAF1	chr6:27856983-27867279	K562	blood:	n/a	chr6:27863647-27863660 chr6:27863652-27863661 chr6:27862695-27862704 chr6:27857910-27857919
6	CREB1	chr6:27857839-27860651	K562	blood:	n/a	n/a
7	POLR2A	chr6:27856821-27873085	K562	blood:	n/a	n/a
8	POLR2A	chr6:27857312-27858906	GM18951	blood:	n/a	n/a
9	POLR2A	chr6:27857203-27859037	MCF-7	breast:	n/a	n/a
10	NFYB	chr6:27858372-27859060	K562	blood:	n/a	chr6:27858647-27858662 chr6:27859045-27859057 chr6:27858649-27858662 chr6:27858651-27858663 chr6:27858650-27858660 chr6:27858648-27858662 chr6:27858647-27858662
11	REST	chr6:27858890-27859553	A549	lung:	n/a	n/a
12	TAF1	chr6:27858263-27859123	MCF-7	breast:	n/a	n/a
13	CBX3	chr6:27857539-27859119	K562	blood:	n/a	n/a
14	POLR2A	chr6:27858740-27859106	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr6:27857317-27858907	SK-N-SH	brain:	n/a	n/a
16	SP1	chr6:27857340-27858974	A549	lung:	n/a	n/a
17	RELA	chr6:27857573-27859227	GM18505	blood:	n/a	n/a
18	POLR2A	chr6:27856943-27864721	H1-hESC	embryonic stem cell:	n/a	n/a
19	ATF2	chr6:27857228-27863693	H1-hESC	embryonic stem cell:	n/a	chr6:27863037-27863048
20	ZNF384	chr6:27858261-27859165	K562	blood:	n/a	n/a
21	TAF1	chr6:27857572-27859099	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr6:27856997-27864751	H1-hESC	embryonic stem cell:	n/a	n/a
23	EP300	chr6:27857535-27858919	SK-N-SH	brain:	n/a	n/a
24	TAF7	chr6:27856262-27863702	H1-hESC	embryonic stem cell:	n/a	n/a
25	SIN3AK20	chr6:27857306-27859047	MCF-7	breast:	n/a	n/a
26	HEY1	chr6:27857544-27863607	K562	blood:	n/a	chr6:27863039-27863048 chr6:27863037-27863046
27	CHD2	chr6:27857359-27861593	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr6:27857279-27863600	K562	blood:	n/a	n/a
29	SP1	chr6:27858331-27858915	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr6:27858317-27859604	MCF10A-Er-Src	breast:	n/a	n/a
31	STAT5A	chr6:27858150-27859112	K562	blood:	n/a	n/a
32	CCNT2	chr6:27858156-27858935	K562	blood:	n/a	n/a
33	SP1	chr6:27857652-27859249	HCT-116	colon:	n/a	n/a
34	TCF12	chr6:27857406-27859011	A549	lung:	n/a	n/a
35	TAF1	chr6:27858205-27859022	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr6:27857169-27859041	GM12878	blood:	n/a	n/a
37	BCLAF1	chr6:27857478-27863716	K562	blood:	n/a	chr6:27863647-27863660 chr6:27863652-27863661 chr6:27862695-27862704 chr6:27857910-27857919
38	MXI1	chr6:27857204-27863823	SK-N-SH	brain:	n/a	n/a
39	POLR2A	chr6:27857138-27863698	GM12878	blood:	n/a	n/a
40	SP1	chr6:27857421-27859224	HCT-116	colon:	n/a	n/a
41	HEY1	chr6:27857159-27865219	K562	blood:	n/a	chr6:27863039-27863048 chr6:27863641-27863656 chr6:27863037-27863046 chr6:27864820-27864829
42	MAX	chr6:27857400-27859200	A549	lung:	n/a	n/a
43	POLR2A	chr6:27857435-27859524	HCT-116	colon:	n/a	n/a
44	POLR2A	chr6:27857499-27858931	H1-neurons	neurons:	n/a	n/a
45	GATA1	chr6:27857541-27863699	PBDE	blood:	n/a	chr6:27863044-27863054
46	HA-E2F1	chr6:27858095-27859173	MCF-7	breast:	n/a	chr6:27859048-27859057
47	TAF1	chr6:27858339-27858953	A549	lung:	n/a	n/a
48	POLR2A	chr6:27857165-27863637	GM12878	blood:	n/a	n/a
49	POLR2A	chr6:27856934-27864217	H1-hESC	embryonic stem cell:	n/a	n/a
50	REST	chr6:27857483-27859052	H1-neurons	neurons:	n/a	chr6:27858599-27858617

No data

(count:48 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26195849..26201222-chr6:27858647..27864324,7	K562	blood:
2	chr6:26199305..26201035-chr6:27856541..27859187,2	K562	blood:
3	chr6:27856359..27859269-chr6:28891133..28894008,2	MCF-7	breast:
4	chr6:27245578..27248207-chr6:27858753..27860256,2	K562	blood:
5	chr6:27840732..27841298-chr6:27858553..27859054,2	NB4	blood:
6	chr6:26203030..26208239-chr6:27858574..27863151,12	MCF-7	breast:
7	chr6:26121961..26124186-chr6:27858294..27861024,3	MCF-7	breast:
8	chr6:27858835..27861043-chr6:28141226..28144128,2	K562	blood:
9	chr10:18939570..18941733-chr6:27856904..27858914,2	MCF-7	breast:
10	chr11:32914073..32914891-chr6:27858213..27859098,2	HCT-116	colon:
11	chr6:27858707..27861368-chr6:28887784..28890166,2	K562	blood:
12	chr17:57923153..57925660-chr6:27857179..27859477,2	MCF-7	breast:
13	chr6:26032242..26033933-chr6:27858634..27862498,4	MCF-7	breast:
14	chr6:27857994..27864853-chr6:28300493..28305532,13	K562	blood:
15	chr17:57917479..57925634-chr6:27855402..27862109,9	MCF-7	breast:
16	chr6:27098129..27102708-chr6:27857691..27863156,15	MCF-7	breast:
17	chr1:11967428..11969173-chr6:27857961..27860830,2	K562	blood:
18	chr6:26154955..26159424-chr6:27857638..27862895,13	MCF-7	breast:
19	chr6:27099529..27101818-chr6:27857109..27860986,3	MCF-7	breast:
20	chr6:26107231..26108901-chr6:27858333..27860619,2	K562	blood:
21	chr16:2203268..2206220-chr6:27857533..27859088,2	K562	blood:
22	chr6:26018945..26024445-chr6:27858774..27864727,7	MCF-7	breast:
23	chr6:27105394..27120060-chr6:27855994..27866393,42	K562	blood:
24	chr6:26211090..26218818-chr6:27857037..27863909,13	K562	blood:
25	chr6:27858159..27860842-chr9:130740925..130743233,2	MCF-7	breast:
26	chr6:26195787..26199567-chr6:27858679..27862629,4	MCF-7	breast:
27	chr6:26270273..26274919-chr6:27857077..27861037,6	MCF-7	breast:
28	chr6:27858753..27860942-chr9:95086192..95088682,2	K562	blood:
29	chr12:69998613..70000144-chr6:27858664..27860434,2	K562	blood:
30	chr6:26122096..26124580-chr6:27856723..27859571,3	K562	blood:
31	chr6:27857150..27860070-chr6:28191777..28193436,2	K562	blood:
32	chr17:55054775..55057118-chr6:27858290..27861016,2	MCF-7	breast:
33	chr6:27857690..27865363-chr6:28300493..28306970,14	K562	blood:
34	chr6:27096288..27105112-chr6:27855525..27865082,32	K562	blood:
35	chr6:27857955..27860857-chr6:28129284..28131805,2	K562	blood:
36	chr6:26019933..26022464-chr6:27857272..27860270,2	MCF-7	breast:
37	chr6:27109893..27116877-chr6:27855936..27864238,12	MCF-7	breast:
38	chr6:27857864..27860590-chr6:28365932..28368425,2	K562	blood:
39	chr6:27094943..27118570-chr6:27854106..27868030,101	K562	blood:
40	chr6:27858116..27862502-chr6:28047404..28050448,4	K562	blood:
41	chr6:26025653..26028340-chr6:27857674..27861144,4	MCF-7	breast:
42	chr6:27857335..27860257-chr7:6521676..6523586,2	MCF-7	breast:
43	chr6:26024607..26035097-chr6:27857610..27864739,17	K562	blood:
44	chr6:26029156..26033137-chr6:27858699..27862567,9	K562	blood:
45	chr1:153939194..153941936-chr6:27857839..27860043,2	MCF-7	breast:
46	chr6:27857264..27863272-chr6:28318615..28325449,9	K562	blood:
47	chr6:26156518..26158542-chr6:27857561..27859684,2	K562	blood:
48	chr6:27857129..27859629-chr6:28105020..28108475,3	K562	blood:

No data

Variant related genes	Relation type
HIST1H3J	TF binding region
HIST1H2BO	TF binding region
ENSG00000131653	Chromatin interaction
ENSG00000269781	Chromatin interaction
ENSG00000188312	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000256018	Chromatin interaction
ENSG00000060749	Chromatin interaction
ENSG00000168298	Chromatin interaction
ENSG00000198339	Chromatin interaction
ENSG00000124529	Chromatin interaction
ENSG00000218690	Chromatin interaction
ENSG00000137185	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000196176	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000272009	Chromatin interaction
ENSG00000143578	Chromatin interaction
ENSG00000167106	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000201524	Chromatin interaction
ENSG00000121064	Chromatin interaction
ENSG00000226314	Chromatin interaction
ENSG00000197279	Chromatin interaction
ENSG00000199004	Chromatin interaction
ENSG00000168274	Chromatin interaction
ENSG00000206630	Chromatin interaction
ENSG00000158691	Chromatin interaction
ENSG00000269293	Chromatin interaction
ENSG00000196866	Chromatin interaction
ENSG00000197409	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000143570	Chromatin interaction
ENSG00000198366	Chromatin interaction
ENSG00000260260	Chromatin interaction
ENSG00000198518	Chromatin interaction
ENSG00000216331	Chromatin interaction
ENSG00000137259	Chromatin interaction
ENSG00000124693	Chromatin interaction
ENSG00000216901	Chromatin interaction
ENSG00000180596	Chromatin interaction
ENSG00000199347	Chromatin interaction
ENSG00000241058	Chromatin interaction
ENSG00000187475	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000198000	Chromatin interaction
ENSG00000180573	Chromatin interaction
ENSG00000187990	Chromatin interaction
ENSG00000198558	Chromatin interaction
ENSG00000168242	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000197846	Chromatin interaction
ENSG00000204713	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs149878	0.87[EUR][1000 genomes]
rs200951	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs200967	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs200988	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs200997	0.82[AFR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs510987	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs200971	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs200971	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs200971	AL022393.7	cis	Muscle Skeletal	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27857000-27863400	Active TSS	Thymus	Thymus
2	chr6:27857000-27863800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr6:27857200-27863800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:27857200-27864000	Active TSS	H9 Cell Line	embryonic stem cell
5	chr6:27857200-27864000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:27857200-27864000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:27857400-27859200	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr6:27857400-27859200	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr6:27857400-27860000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:27857400-27864000	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr6:27857400-27864400	Active TSS	H1 Cell Line	embryonic stem cell
12	chr6:27857400-27864400	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr6:27857600-27859600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr6:27857600-27861000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr6:27857600-27864000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr6:27857800-27861000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr6:27857800-27863600	Active TSS	iPS-18 Cell Line	embryonic stem cell
18	chr6:27857800-27863800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr6:27857800-27864000	Active TSS	A549	lung
20	chr6:27858000-27859000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:27858000-27859000	Flanking Active TSS	Primary B cells from peripheral blood	blood
22	chr6:27858000-27859000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
23	chr6:27858000-27859000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
24	chr6:27858000-27859000	Enhancers	Spleen	Spleen
25	chr6:27858000-27859200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr6:27858000-27859200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
27	chr6:27858000-27859200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
28	chr6:27858000-27859200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
29	chr6:27858000-27859400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
30	chr6:27858000-27860200	Active TSS	Fetal Brain Female	brain
31	chr6:27858000-27860800	Flanking Active TSS	Primary hematopoietic stem cells	blood
32	chr6:27858000-27863600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr6:27858000-27863600	Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr6:27858000-27863600	Active TSS	Fetal Lung	lung
35	chr6:27858000-27864000	Active TSS	ES-I3 Cell Line	embryonic stem cell
36	chr6:27858000-27864000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr6:27858200-27859200	Active TSS	Fetal Intestine Small	intestine
38	chr6:27858200-27859200	Active TSS	Placenta Amnion	Placenta Amnion
39	chr6:27858200-27863600	Active TSS	Fetal Intestine Large	intestine
40	chr6:27858200-27863800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr6:27858200-27863800	Active TSS	Brain Germinal Matrix	brain
42	chr6:27858200-27864000	Active TSS	NHLF	lung
43	chr6:27858200-27864200	Active TSS	Fetal Kidney	kidney
44	chr6:27858400-27859000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr6:27858400-27859000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr6:27858400-27859000	Active TSS	Duodenum Mucosa	Duodenum
47	chr6:27858400-27859000	Active TSS	Fetal Heart	heart
48	chr6:27858400-27859000	Active TSS	HSMM	muscle
49	chr6:27858400-27859200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr6:27858400-27859200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

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