Variant report

Variant	rs2064093
Chromosome Location	chr6:27442247-27442248
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:26158037..26160369-chr6:27440864..27442625,2	K562	blood:
2	chr6:27356277..27359093-chr6:27439899..27443040,4	MCF-7	breast:
3	chr6:27114670..27118026-chr6:27440668..27442830,6	K562	blood:
4	chr6:27261990..27263611-chr6:27441334..27443428,2	K562	blood:
5	chr6:27148927..27151021-chr6:27440997..27443273,2	K562	blood:
6	chr6:27112142..27119511-chr6:27439134..27442830,9	K562	blood:
7	chr6:27143738..27145587-chr6:27441019..27442990,2	K562	blood:

Variant related genes	Relation type
ENSG00000124613	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000265565	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1011665	0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap]
rs10946915	0.88[AMR][1000 genomes]
rs10946935	0.86[LWK][hapmap];0.88[YRI][hapmap]
rs10946940	0.86[LWK][hapmap];0.80[YRI][hapmap]
rs12526495	0.86[AMR][1000 genomes]
rs12529458	0.86[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap]
rs12529756	0.91[ASN][1000 genomes]
rs12663650	1.00[YRI][hapmap]
rs12664996	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap]
rs13220817	0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap]
rs1883403	0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap]
rs2205829	0.91[ASN][1000 genomes]
rs2235232	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2393962	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2393963	0.91[ASN][1000 genomes]
rs2393964	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4711152	0.89[AMR][1000 genomes]
rs4711154	1.00[ASN][1000 genomes]
rs4711155	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713098	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4713099	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6456799	0.80[YRI][hapmap]
rs6913166	0.87[GIH][hapmap];0.84[MEX][hapmap]
rs6914864	0.87[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap]
rs6915266	0.88[LWK][hapmap];0.88[YRI][hapmap]
rs7761966	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9393813	0.95[CHB][hapmap];0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	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
3	nsv830617	chr6:27424769-27598595	Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv883508	chr6:27434220-27455625	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2064093	ZNF204P	cis	parietal	SCAN
rs2064093	ZNF391	cis	cerebellum	SCAN
rs2064093	ZNF391	cis	lung	GTEx
rs2064093	HIST1H2AJ	cis	cerebellum	SCAN
rs2064093	ZNF391	cis	parietal	SCAN
rs2064093	BTN3A3	cis	cerebellum	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27439000-27442800	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr6:27439200-27442400	Active TSS	A549	lung
3	chr6:27439200-27442600	Active TSS	H1 Cell Line	embryonic stem cell
4	chr6:27439400-27442400	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr6:27441400-27445000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr6:27441400-27445000	Weak transcription	Aorta	Aorta
7	chr6:27441400-27445200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr6:27441400-27445400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr6:27441400-27446000	Weak transcription	Gastric	stomach
10	chr6:27441400-27446000	Weak transcription	Lung	lung
11	chr6:27441400-27446400	Weak transcription	Small Intestine	intestine
12	chr6:27441400-27446800	Weak transcription	Spleen	Spleen
13	chr6:27441600-27442800	Enhancers	Dnd41	blood
14	chr6:27441600-27444800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr6:27441600-27444800	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr6:27441600-27445000	Weak transcription	Primary B cells from peripheral blood	blood
17	chr6:27441600-27445000	Weak transcription	Primary hematopoietic stem cells	blood
18	chr6:27441600-27445000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr6:27441600-27445000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr6:27441600-27445200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr6:27441600-27445200	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr6:27441600-27445200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr6:27441600-27445200	Weak transcription	NHDF-Ad	bronchial
24	chr6:27441600-27445400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr6:27441600-27445400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr6:27441600-27445400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr6:27441600-27445400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr6:27441600-27445600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr6:27441600-27445600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr6:27441600-27445600	Weak transcription	Brain Hippocampus Middle	brain
31	chr6:27441600-27445600	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr6:27441600-27445600	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr6:27441600-27445800	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr6:27441600-27445800	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr6:27441600-27446000	Weak transcription	Left Ventricle	heart
36	chr6:27441600-27446000	Weak transcription	HSMMtube	muscle
37	chr6:27441800-27445000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:27441800-27445000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr6:27441800-27445000	Weak transcription	Primary B cells from cord blood	blood
40	chr6:27441800-27445000	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr6:27441800-27445000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr6:27441800-27445000	Weak transcription	Psoas Muscle	Psoas
43	chr6:27441800-27445200	Weak transcription	Primary T cells from cord blood	blood
44	chr6:27441800-27445200	Weak transcription	Brain Substantia Nigra	brain
45	chr6:27441800-27445200	Weak transcription	Fetal Stomach	stomach
46	chr6:27441800-27445200	Weak transcription	Osteobl	bone
47	chr6:27441800-27445400	Weak transcription	Brain Anterior Caudate	brain
48	chr6:27441800-27445400	Weak transcription	Fetal Lung	lung
49	chr6:27441800-27445400	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr6:27441800-27445600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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