Variant report

Variant	rs6478969
Chromosome Location	chr9:101819532-101819533
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:101797638..101801423-chr9:101817658..101821818,3	K562	blood:

Variant related genes	Relation type
ENSG00000204291	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10512262	0.93[CEU][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.82[ASN][1000 genomes]
rs12001981	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12352174	1.00[CEU][hapmap];0.83[ASN][1000 genomes]
rs13291453	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13296166	0.93[CEU][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.84[ASN][1000 genomes]
rs13302368	0.93[CEU][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.84[ASN][1000 genomes]
rs1537505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1537506	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[MKK][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16918146	0.81[ASN][1000 genomes]
rs16918148	0.92[CEU][hapmap];0.84[ASN][1000 genomes]
rs16918154	0.84[ASN][1000 genomes]
rs16918163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2067986	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34382379	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34654420	0.84[ASN][1000 genomes]
rs34749011	0.82[ASN][1000 genomes]
rs35413276	0.82[ASN][1000 genomes]
rs4563947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4631520	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7019613	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7030799	0.81[CEU][hapmap]
rs7036916	1.00[CEU][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.84[ASN][1000 genomes]
rs7047475	0.81[CEU][hapmap]
rs7851079	1.00[CEU][hapmap]
rs7854112	1.00[CEU][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.82[ASN][1000 genomes]
rs7857774	1.00[CEU][hapmap];0.93[CHB][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs928522	0.93[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893618	chr9:101800106-101886071	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6478969	GALNT12	cis	lymphoblastoid	seeQTL
rs6478969	COL15A1	cis	lymphoblastoid	seeQTL

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101782000-101819800	Weak transcription	Colonic Mucosa	Colon
2	chr9:101793800-101837600	Weak transcription	Psoas Muscle	Psoas
3	chr9:101798400-101819800	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr9:101804000-101820000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr9:101805800-101820600	Weak transcription	Right Ventricle	heart
6	chr9:101807000-101831800	Strong transcription	Fetal Muscle Trunk	muscle
7	chr9:101807600-101831800	Strong transcription	Fetal Muscle Leg	muscle
8	chr9:101807800-101819800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr9:101809200-101821600	Weak transcription	Brain Anterior Caudate	brain
10	chr9:101810600-101819800	Enhancers	Primary T cells fromperipheralblood	blood
11	chr9:101811200-101820000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr9:101813200-101833000	Weak transcription	Lung	lung
13	chr9:101813600-101825600	Weak transcription	Aorta	Aorta
14	chr9:101814200-101820200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr9:101814200-101826600	Weak transcription	Fetal Intestine Large	intestine
16	chr9:101814200-101829400	Weak transcription	Fetal Intestine Small	intestine
17	chr9:101814400-101820200	Enhancers	Thymus	Thymus
18	chr9:101814600-101819600	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr9:101814800-101820000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr9:101814800-101820200	Weak transcription	Right Atrium	heart
21	chr9:101815600-101819800	Enhancers	HSMM	muscle
22	chr9:101815600-101820600	Strong transcription	Stomach Smooth Muscle	stomach
23	chr9:101815600-101821400	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr9:101816000-101819800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr9:101816200-101844200	Weak transcription	Gastric	stomach
26	chr9:101816600-101819800	Weak transcription	Duodenum Mucosa	Duodenum
27	chr9:101816600-101820000	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr9:101816800-101819800	Enhancers	NH-A	brain
29	chr9:101816800-101821200	Enhancers	HMEC	breast
30	chr9:101816800-101822400	Enhancers	Osteobl	bone
31	chr9:101817000-101820200	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr9:101817000-101821600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr9:101817400-101819800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr9:101817400-101819800	Enhancers	NHEK	skin
35	chr9:101817400-101820000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr9:101817600-101819600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr9:101817600-101819800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr9:101817600-101819800	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr9:101817600-101819800	Enhancers	K562	blood
40	chr9:101817600-101820000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr9:101817600-101820200	Enhancers	Primary B cells from peripheral blood	blood
42	chr9:101817600-101821000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr9:101817800-101819600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr9:101817800-101819800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr9:101817800-101819800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr9:101818000-101819600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr9:101818000-101834800	Weak transcription	Pancreas	Pancrea
48	chr9:101818200-101820000	Enhancers	Primary hematopoietic stem cells	blood
49	chr9:101818400-101819600	Enhancers	Primary B cells from cord blood	blood
50	chr9:101818400-101820400	Enhancers	Fetal Thymus	thymus

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