Variant report

Variant	rs6565182
Chromosome Location	chr16:30374381-30374382
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:30373103..30376469-chr16:30389093..30391180,4	K562	blood:
2	chr16:30371819..30375915-chr16:30388741..30392397,3	K562	blood:
3	chr16:30368801..30385970-chr16:30403825..30413311,30	MCF-7	breast:

Variant related genes	Relation type
ENSG00000180035	Chromatin interaction
ENSG00000180096	Chromatin interaction
ENSG00000180209	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11150586	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs1132812	1.00[YRI][hapmap]
rs11642676	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11644392	0.90[ASN][1000 genomes]
rs11645581	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11646130	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11862806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11863150	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs12446288	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs12447833	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12921440	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs12922786	0.88[ASN][1000 genomes]
rs12930787	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13333093	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs2911213	0.87[ASN][1000 genomes]
rs35480350	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35598865	1.00[JPT][hapmap]
rs3574	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4465620	0.84[CEU][hapmap];0.82[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs4471699	0.93[ASN][1000 genomes]
rs4787642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4787643	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4788408	0.93[ASN][1000 genomes]
rs4788409	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4788411	0.81[EUR][1000 genomes]
rs4788413	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4788414	0.82[EUR][1000 genomes]
rs62055459	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6565176	0.88[GIH][hapmap]
rs6565178	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6565180	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6565183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs68051857	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7186541	0.90[ASN][1000 genomes]
rs7195216	0.90[ASN][1000 genomes]
rs7203359	0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73532600	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7404371	0.88[ASN][1000 genomes]
rs8046445	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8049108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8050176	0.93[ASN][1000 genomes]
rs8050812	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs8051096	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8060853	0.82[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9921711	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065915	chr16:29967090-30486120	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	229 gene(s)	inside rSNPs	diseases
2	nsv542897	chr16:29967090-30486120	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	229 gene(s)	inside rSNPs	diseases
3	esv2758420	chr16:30073955-30383280	Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
4	esv2758642	chr16:30073955-30383280	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
5	nsv1056897	chr16:30363683-30457504	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases
6	nsv905724	chr16:30368591-30438930	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
7	nsv532531	chr16:30370550-30581820	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	113 gene(s)	inside rSNPs	diseases
8	nsv827612	chr16:30371538-30429862	Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6565182	TBX6	cis	parietal	SCAN
rs6565182	MAPK3	cis	parietal	SCAN
rs6565182	GDPD3	cis	cerebellum	SCAN
rs6565182	IMAA///LOC440345///LOC440354///LOC595101///	N/A	lymphoblastoid	RTeQTL
rs6565182	SEPHS2	cis	cerebellum	SCAN
rs6565182	BOLA2///LOC440354///LOC595101	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30367400-30377200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr16:30367400-30377200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr16:30367600-30375200	Weak transcription	Small Intestine	intestine
4	chr16:30367600-30378600	Weak transcription	Fetal Kidney	kidney
5	chr16:30367600-30378600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr16:30367600-30378800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr16:30367800-30378000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr16:30368000-30376800	Strong transcription	Skeletal Muscle Male	skeletal muscle
9	chr16:30368000-30378600	Strong transcription	Fetal Stomach	stomach
10	chr16:30368200-30374400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr16:30368200-30376000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr16:30368200-30376000	Strong transcription	Fetal Muscle Trunk	muscle
13	chr16:30368200-30376400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr16:30368200-30376800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr16:30368200-30377200	Strong transcription	Sigmoid Colon	Sigmoid Colon
16	chr16:30368200-30377600	Strong transcription	Duodenum Smooth Muscle	Duodenum
17	chr16:30368200-30378000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr16:30368200-30378200	Strong transcription	Lung	lung
19	chr16:30368200-30378600	Strong transcription	Fetal Intestine Small	intestine
20	chr16:30368200-30379000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr16:30368400-30376000	Weak transcription	Fetal Brain Male	brain
22	chr16:30368400-30376400	Strong transcription	Stomach Smooth Muscle	stomach
23	chr16:30368400-30376400	Strong transcription	Spleen	Spleen
24	chr16:30368400-30377200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr16:30368400-30377200	Strong transcription	Colon Smooth Muscle	Colon
26	chr16:30368400-30377400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr16:30368400-30377800	Strong transcription	Thymus	Thymus
28	chr16:30368400-30378000	Strong transcription	Fetal Muscle Leg	muscle
29	chr16:30368400-30378000	Strong transcription	Fetal Thymus	thymus
30	chr16:30368400-30378200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr16:30368400-30378800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr16:30368400-30378800	Weak transcription	HSMMtube	muscle
33	chr16:30368600-30374600	Strong transcription	Right Ventricle	heart
34	chr16:30368600-30374800	Strong transcription	NHEK	skin
35	chr16:30368600-30375800	Weak transcription	Primary hematopoietic stem cells	blood
36	chr16:30368600-30377200	Strong transcription	Duodenum Mucosa	Duodenum
37	chr16:30368600-30377600	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr16:30368600-30377800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr16:30368600-30378000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr16:30368600-30378000	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr16:30368600-30378400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr16:30368800-30376600	Strong transcription	Brain Hippocampus Middle	brain
43	chr16:30368800-30377000	Strong transcription	Primary B cells from peripheral blood	blood
44	chr16:30368800-30377000	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr16:30368800-30377200	Strong transcription	Osteobl	bone
46	chr16:30368800-30378600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr16:30369000-30374400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr16:30369000-30376200	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr16:30369000-30377200	Strong transcription	Adipose Nuclei	Adipose
50	chr16:30369000-30377400	Strong transcription	Rectal Mucosa Donor 31	rectum

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