Variant report

Variant	rs200951
Chromosome Location	chr6:27835930-27835931
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 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	MXI1	chr6:27831650-27836500	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr6:27832456-27836599	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr6:27835709-27836049	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:16 , 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	chr6:26154866..26157028-chr6:27832028..27836151,3	MCF-7	breast:
4	chr6:26249129..26252003-chr6:27832611..27836378,6	MCF-7	breast:
5	chr6:26156108..26158898-chr6:27832756..27836611,3	MCF-7	breast:
6	chr6:27113081..27116777-chr6:27832860..27836046,4	K562	blood:
7	chr6:26033297..26035200-chr6:27833856..27836117,3	MCF-7	breast:
8	chr6:27105570..27109142-chr6:27832678..27836176,3	K562	blood:
9	chr6:27834624..27836124-chr7:99722099..99724739,2	MCF-7	breast:
10	chr6:26044265..26046503-chr6:27834017..27836277,2	MCF-7	breast:
11	chr6:26019660..26022685-chr6:27833901..27836758,3	MCF-7	breast:
12	chr6:26123459..26125455-chr6:27834569..27837416,2	MCF-7	breast:
13	chr1:149855909..149858308-chr6:27833822..27835971,2	MCF-7	breast:
14	chr16:4663445..4665916-chr6:27834145..27836986,3	MCF-7	breast:
15	chr1:16840036..16842043-chr6:27834742..27837032,2	MCF-7	breast:
16	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
ENSG00000265565	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000214309	Chromatin interaction
ENSG00000153443	Chromatin interaction
ENSG00000256316	Chromatin interaction
ENSG00000261135	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000196532	Chromatin interaction
ENSG00000206652	Chromatin interaction
ENSG00000137259	Chromatin interaction
ENSG00000180596	Chromatin interaction
ENSG00000198366	Chromatin interaction
ENSG00000196176	Chromatin interaction
ENSG00000168298	Chromatin interaction
ENSG00000197459	Chromatin interaction
ENSG00000163399	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000180573	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000198339	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 23 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs149878	0.89[EUR][1000 genomes]
rs149897	0.86[CEU][hapmap]
rs149942	0.86[CEU][hapmap]
rs149944	0.86[CEU][hapmap]
rs149945	0.86[CEU][hapmap]
rs149959	0.86[CEU][hapmap]
rs149972	0.86[CEU][hapmap]
rs149989	0.86[CEU][hapmap]
rs156739	0.86[CEU][hapmap]
rs200967	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs200971	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs200988	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs200994	0.82[CEU][hapmap];0.86[TSI][hapmap]
rs200997	0.94[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.97[LWK][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs510987	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9295747	0.91[LWK][hapmap]

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:23)

SNP	Gene	Cis/trans	Tissue	Source
rs200951	ZNF323	cis	Brain Pons	GTEx
rs200951	ZNF323	cis	cerebellum	SCAN
rs200951	BTN2A1	cis	parietal	SCAN
rs200951	ZKSCAN3	cis	cerebellum	SCAN
rs200951	NRSN1	cis	cerebellum	SCAN
rs200951	ZNF323	cis	parietal	SCAN
rs200951	OR2B8P	cis	Thyroid	GTEx
rs200951	ZKSCAN3	cis	parietal	SCAN
rs200951	HIST1H3C	cis	cerebellum	SCAN
rs200951	ZNF187	cis	cerebellum	SCAN
rs200951	ZSCAN31	cis	Nerve Tibial	GTEx
rs200951	ZNF323	cis	Frontal Cortex	GTEx
rs200951	AL022393.7	cis	Nerve Tibial	GTEx
rs200951	ZNF192	cis	parietal	SCAN
rs200951	ZNF204P	cis	parietal	SCAN
rs200951	LRRC16A	cis	parietal	SCAN
rs200951	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs200951	ZNF192	cis	cerebellum	SCAN
rs200951	RP1-265C24.5	cis	Muscle Skeletal	GTEx
rs200951	ZSCAN23	cis	cerebellum	SCAN
rs200951	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs200951	AL022393.7	cis	Muscle Skeletal	GTEx
rs200951	ZNF323	cis	Cerebellum	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27832200-27836000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr6:27833200-27836000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr6:27833200-27836200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr6:27833400-27836000	Flanking Active TSS	Primary T cells from cord blood	blood
5	chr6:27833400-27836000	Flanking Active TSS	Primary hematopoietic stem cells	blood
6	chr6:27833400-27836000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr6:27834000-27836000	Flanking Active TSS	NHEK	skin
8	chr6:27835000-27836000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr6:27835000-27836000	Active TSS	Fetal Intestine Large	intestine
10	chr6:27835200-27836000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:27835200-27836000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr6:27835200-27838200	Weak transcription	Lung	lung
13	chr6:27835400-27836000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr6:27835400-27836000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
15	chr6:27835400-27836000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
16	chr6:27835400-27836000	Bivalent Enhancer	Brain Substantia Nigra	brain
17	chr6:27835400-27836000	Flanking Active TSS	Fetal Lung	lung
18	chr6:27835400-27836000	Flanking Active TSS	NH-A	brain
19	chr6:27835400-27838200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr6:27835400-27838800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr6:27835400-27839000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr6:27835400-27839000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr6:27835400-27839400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr6:27835400-27839600	Weak transcription	Colonic Mucosa	Colon
25	chr6:27835400-27839600	Weak transcription	Esophagus	oesophagus
26	chr6:27835400-27839600	Weak transcription	Pancreas	Pancrea
27	chr6:27835600-27836000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:27835600-27836000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
29	chr6:27835600-27836000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr6:27835600-27836000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr6:27835600-27836000	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr6:27835600-27836000	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr6:27835600-27836000	Enhancers	Primary B cells from peripheral blood	blood
34	chr6:27835600-27836000	Enhancers	Primary T cells fromperipheralblood	blood
35	chr6:27835600-27836000	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr6:27835600-27836000	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr6:27835600-27836000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr6:27835600-27836000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr6:27835600-27836000	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr6:27835600-27836000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr6:27835600-27836000	Enhancers	Adipose Nuclei	Adipose
42	chr6:27835600-27836000	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
43	chr6:27835600-27836000	Enhancers	Duodenum Mucosa	Duodenum
44	chr6:27835600-27836000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr6:27835600-27836000	Flanking Active TSS	Fetal Thymus	thymus
46	chr6:27835600-27836000	Bivalent Enhancer	HepG2	liver
47	chr6:27835600-27836000	Enhancers	NHLF	lung
48	chr6:27835600-27836200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
49	chr6:27835600-27836200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
50	chr6:27835600-27836200	Flanking Active TSS	Brain Germinal Matrix	brain

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