Variant report

Variant	rs1884947
Chromosome Location	chr6:26553273-26553274
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:24)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:24 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26550749..26553522-chr6:26553841..26558660,4	K562	blood:
2	chr6:26204395..26206549-chr6:26552020..26554582,2	K562	blood:
3	chr6:26546606..26549431-chr6:26551498..26554971,7	K562	blood:
4	chr6:26552134..26560768-chr6:26592842..26598560,12	K562	blood:
5	chr6:26553266..26555842-chr6:26556342..26558941,2	K562	blood:
6	chr6:26315914..26318204-chr6:26552623..26555591,2	MCF-7	breast:
7	chr6:26552045..26554555-chr6:27112224..27114083,2	MCF-7	breast:
8	chr6:26538455..26540998-chr6:26551763..26554310,5	MCF-7	breast:
9	chr6:26053729..26056737-chr6:26552684..26556029,5	K562	blood:
10	chr6:26204395..26207558-chr6:26552020..26555399,3	K562	blood:
11	chr6:26215416..26220761-chr6:26552496..26557332,5	K562	blood:
12	chr6:26547747..26549536-chr6:26553157..26556049,2	MCF-7	breast:
13	chr6:26541650..26546578-chr6:26547247..26553909,5	MCF-7	breast:
14	chr6:26551841..26553522-chr6:26554319..26556111,2	K562	blood:
15	chr6:26311888..26313788-chr6:26552571..26554289,2	MCF-7	breast:
16	chr6:26553141..26555933-chr6:26567279..26569954,2	MCF-7	breast:
17	chr6:26551317..26553422-chr6:26555565..26558257,2	MCF-7	breast:
18	chr6:26550881..26553679-chr6:26594606..26597550,2	MCF-7	breast:
19	chr6:26537424..26539993-chr6:26551057..26554876,4	MCF-7	breast:
20	chr6:26553067..26555793-chr6:27098246..27101919,3	K562	blood:
21	chr6:26284182..26287144-chr6:26550999..26553713,2	K562	blood:
22	chr6:26311071..26313329-chr6:26552209..26554429,3	K562	blood:
23	chr6:26401296..26404115-chr6:26552128..26554216,2	K562	blood:
24	chr6:26510913..26513232-chr6:26552632..26554194,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000026950	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000198518	Chromatin interaction
ENSG00000187837	Chromatin interaction
ENSG00000168274	Chromatin interaction
ENSG00000187990	Chromatin interaction
ENSG00000182952	Chromatin interaction
ENSG00000146109	Chromatin interaction
ENSG00000158406	Chromatin interaction
ENSG00000124635	Chromatin interaction

Extended variants
information (count: 128 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs1001687	0.89[EUR][1000 genomes]
rs10214634	0.94[EUR][1000 genomes]
rs10223789	0.84[EUR][1000 genomes]
rs10223792	0.84[EUR][1000 genomes]
rs1027203	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1027204	0.81[CHB][hapmap]
rs10484442	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.87[TSI][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1056347	0.84[EUR][1000 genomes]
rs1056667	1.00[CEU][hapmap];0.89[GIH][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs1056668	0.92[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1078679	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs10946834	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs10946835	1.00[CEU][hapmap];0.89[GIH][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs10946837	0.94[EUR][1000 genomes]
rs11752946	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11754138	0.84[EUR][1000 genomes]
rs11756120	0.83[EUR][1000 genomes]
rs12526680	1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12663883	0.88[EUR][1000 genomes]
rs12663894	0.87[EUR][1000 genomes]
rs12665431	0.87[EUR][1000 genomes]
rs1321479	0.96[CEU][hapmap];0.85[GIH][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs1321480	0.84[EUR][1000 genomes]
rs1321481	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs1321482	1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.80[TSI][hapmap];0.88[EUR][1000 genomes]
rs1407045	0.81[TSI][hapmap]
rs1535276	1.00[CEU][hapmap];0.89[GIH][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs1535277	0.82[EUR][1000 genomes]
rs1570059	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[EUR][1000 genomes]
rs1570060	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[EUR][1000 genomes]
rs1570061	1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.80[TSI][hapmap];0.88[EUR][1000 genomes]
rs16891824	1.00[YRI][hapmap]
rs1741740	1.00[YRI][hapmap]
rs1796521	1.00[YRI][hapmap]
rs1884946	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs1884948	0.92[EUR][1000 genomes]
rs1884949	0.92[EUR][1000 genomes]
rs1977201	0.89[EUR][1000 genomes]
rs2172007	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2208331	0.83[EUR][1000 genomes]
rs2224380	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.87[TSI][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2255070	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2393670	1.00[CEU][hapmap];0.89[GIH][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs2451711	0.81[CHB][hapmap]
rs2451741	0.81[CHB][hapmap]
rs2494692	0.80[CHB][hapmap]
rs2494701	0.81[CHB][hapmap]
rs2498380	0.81[CHB][hapmap]
rs2504566	0.81[CHB][hapmap]
rs2504567	0.81[CHB][hapmap]
rs2504571	0.81[CHB][hapmap]
rs2504600	0.81[CHB][hapmap]
rs28558133	0.80[EUR][1000 genomes]
rs35355150	0.86[EUR][1000 genomes]
rs3736781	1.00[CEU][hapmap];0.87[GIH][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs3736782	1.00[CEU][hapmap];0.89[GIH][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs3800303	0.81[CHB][hapmap]
rs4368798	0.81[CHB][hapmap]
rs4573	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs4713006	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs4713008	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs4871	1.00[CEU][hapmap];0.89[GIH][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs55930917	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6456733	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes]
rs6456734	0.91[EUR][1000 genomes]
rs6456735	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs6903973	1.00[CEU][hapmap];0.91[GIH][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs6909277	0.88[EUR][1000 genomes]
rs6910899	0.84[EUR][1000 genomes]
rs6910930	0.84[EUR][1000 genomes]
rs6913398	0.92[EUR][1000 genomes]
rs6913462	0.88[EUR][1000 genomes]
rs6913877	0.88[EUR][1000 genomes]
rs6918360	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[EUR][1000 genomes]
rs6918506	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[EUR][1000 genomes]
rs6918854	1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.80[TSI][hapmap];0.88[EUR][1000 genomes]
rs6922824	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.87[TSI][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6924838	0.92[EUR][1000 genomes]
rs6924865	0.87[GIH][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs6925703	1.00[CEU][hapmap];0.89[GIH][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs6925783	0.89[EUR][1000 genomes]
rs6925895	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs6926629	1.00[CEU][hapmap];0.89[GIH][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs6930120	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6932156	0.92[EUR][1000 genomes]
rs6932350	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6932865	0.92[EUR][1000 genomes]
rs6933176	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6940053	0.93[EUR][1000 genomes]
rs6940188	0.93[EUR][1000 genomes]
rs6941022	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.87[TSI][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs767471	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7753565	1.00[CEU][hapmap];0.86[CHB][hapmap]
rs7767847	0.81[CHB][hapmap]
rs9295694	0.83[EUR][1000 genomes]
rs9295695	1.00[CEU][hapmap];0.89[GIH][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs9295698	0.93[EUR][1000 genomes]
rs9357010	1.00[CEU][hapmap];0.89[GIH][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs9358954	0.83[EUR][1000 genomes]
rs9379887	0.84[EUR][1000 genomes]
rs9393729	1.00[CEU][hapmap];0.89[GIH][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs9393731	0.84[EUR][1000 genomes]
rs9393732	0.84[EUR][1000 genomes]
rs9461259	0.82[EUR][1000 genomes]
rs9461267	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs9461270	1.00[CEU][hapmap];0.89[GIH][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs9461271	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.87[TSI][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9461272	1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[EUR][1000 genomes]
rs9467774	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs9467775	0.83[EUR][1000 genomes]
rs9467776	0.83[EUR][1000 genomes]
rs9467778	0.90[EUR][1000 genomes]
rs9467779	1.00[CEU][hapmap];0.89[GIH][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs9467782	1.00[CEU][hapmap];0.89[GIH][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs9467783	1.00[CEU][hapmap];0.89[GIH][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs9467784	0.92[EUR][1000 genomes]
rs9467787	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9467791	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[GIH][hapmap];0.93[EUR][1000 genomes]
rs9467796	0.92[EUR][1000 genomes]
rs9467797	0.92[EUR][1000 genomes]
rs9467798	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs9467799	0.85[EUR][1000 genomes]
rs9467800	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[EUR][1000 genomes]
rs9467802	0.84[EUR][1000 genomes]
rs9467810	0.81[CHB][hapmap]
rs9986382	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.87[TSI][hapmap];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs1884947	BTN3A3	cis	cerebellum	SCAN
rs1884947	ZNF322B	trans	multi-tissue	Pritchard
rs1884947	HCG11	cis	uninvolved skin	skin_eQTL
rs1884947	BTN3A3	cis	parietal	SCAN
rs1884947	HCG11	cis	normal skin	skin_eQTL
rs1884947	HMGN4	cis	Whole Blood	GTEx
rs1884947	RP11-457M11.5	cis	Artery Tibial	GTEx
rs1884947	HIST1H2BD	cis	parietal	SCAN
rs1884947	BTN3A2	cis	lymphoblastoid	seeQTL
rs1884947	BTN3A2	cis	cerebellum	SCAN
rs1884947	ZNF322B	trans	lymphoblastoid	seeQTL
rs1884947	BTN3A2	cis	multi-tissue	Pritchard
rs1884947	ZNF204P	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26551000-26553400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:26551000-26556400	Weak transcription	Spleen	Spleen
3	chr6:26551200-26553400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:26551200-26553400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr6:26551200-26553400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr6:26551200-26553400	Weak transcription	Liver	Liver
7	chr6:26551200-26553400	Weak transcription	Colonic Mucosa	Colon
8	chr6:26551200-26553400	Weak transcription	Esophagus	oesophagus
9	chr6:26551200-26553400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr6:26551200-26553600	Weak transcription	Stomach Mucosa	stomach
11	chr6:26551200-26553800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr6:26551200-26553800	Weak transcription	Small Intestine	intestine
13	chr6:26551200-26554000	Weak transcription	Pancreas	Pancrea
14	chr6:26551200-26556200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:26551600-26553400	Weak transcription	Placenta	Placenta
16	chr6:26552600-26553400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr6:26552600-26553600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr6:26552600-26553800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr6:26552600-26556200	Active TSS	GM12878-XiMat	blood
20	chr6:26552600-26556400	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr6:26552600-26556800	Active TSS	NHDF-Ad	bronchial
22	chr6:26552800-26553400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr6:26552800-26553400	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr6:26552800-26553400	Flanking Active TSS	Brain Germinal Matrix	brain
25	chr6:26552800-26553400	Flanking Active TSS	Dnd41	blood
26	chr6:26552800-26553400	Active TSS	HepG2	liver
27	chr6:26552800-26554600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr6:26552800-26556400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr6:26552800-26557200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr6:26553000-26553400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
31	chr6:26553000-26553400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr6:26553000-26553400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr6:26553000-26553400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr6:26553000-26553400	Flanking Active TSS	Brain Angular Gyrus	brain
35	chr6:26553000-26553400	Flanking Active TSS	Brain Anterior Caudate	brain
36	chr6:26553000-26553400	Flanking Active TSS	Brain Cingulate Gyrus	brain
37	chr6:26553000-26553400	Flanking Active TSS	Fetal Brain Female	brain
38	chr6:26553000-26553400	Enhancers	Fetal Heart	heart
39	chr6:26553000-26553400	Flanking Active TSS	Fetal Kidney	kidney
40	chr6:26553000-26553600	Flanking Active TSS	Primary B cells from cord blood	blood
41	chr6:26553000-26553600	Flanking Active TSS	Primary hematopoietic stem cells	blood
42	chr6:26553000-26553600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
43	chr6:26553000-26553600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
44	chr6:26553000-26554200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr6:26553000-26554600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr6:26553000-26554600	Active TSS	Muscle Satellite Cultured Cells	--
47	chr6:26553000-26555200	Flanking Active TSS	Primary T cells from cord blood	blood
48	chr6:26553000-26555200	Active TSS	Aorta	Aorta
49	chr6:26553000-26555200	Active TSS	Stomach Smooth Muscle	stomach
50	chr6:26553000-26556200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

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