Variant report

Variant	rs6796790
Chromosome Location	chr3:48780317-48780318
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF384	chr3:48779673-48780413	K562	blood:	n/a	n/a
2	TBL1XR1	chr3:48780234-48780367	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:48698968..48701587-chr3:48778820..48781194,2	K562	blood:
2	chr3:48777662..48781214-chr3:48954479..48957215,3	K562	blood:
3	chr3:48778919..48781292-chr3:49044225..49047223,2	K562	blood:
4	chr3:48777544..48781186-chr3:48954650..48958375,5	K562	blood:
5	chr3:48778330..48780434-chr3:48788133..48790019,2	K562	blood:

No data

Variant related genes	Relation type
IP6K2	TF binding region
ENSG00000228350	Chromatin interaction
ENSG00000177479	Chromatin interaction
ENSG00000114302	Chromatin interaction
ENSG00000008300	Chromatin interaction
ENSG00000178252	Chromatin interaction
ENSG00000221883	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 35 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10780033	0.82[YRI][hapmap]
rs10865953	1.00[CEU][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs11130176	0.82[YRI][hapmap]
rs1134591	0.82[YRI][hapmap]
rs12493289	0.82[YRI][hapmap]
rs12632533	1.00[CEU][hapmap];0.83[TSI][hapmap]
rs12715430	0.80[EUR][1000 genomes]
rs14018	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes]
rs4858799	0.84[EUR][1000 genomes]
rs4858800	1.00[CEU][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs4858830	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs4974079	0.93[YRI][hapmap]
rs4974085	0.82[YRI][hapmap]
rs4974087	0.93[YRI][hapmap]
rs4974088	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs6442129	0.84[EUR][1000 genomes]
rs6442130	0.82[ASW][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes]
rs6442131	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6446252	0.92[YRI][hapmap]
rs6446253	0.84[YRI][hapmap]
rs6766238	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6801211	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6806356	1.00[CEU][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs7373072	1.00[CEU][hapmap];0.96[YRI][hapmap]
rs7429596	0.91[EUR][1000 genomes]
rs7430501	0.82[YRI][hapmap]
rs7431857	0.82[YRI][hapmap]
rs7610519	0.85[EUR][1000 genomes]
rs7621226	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7627404	0.93[YRI][hapmap]
rs7639370	0.92[EUR][1000 genomes]
rs7641050	0.88[EUR][1000 genomes]
rs7653408	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs9284885	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9311430	0.82[YRI][hapmap]
rs9311431	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs9311433	0.82[YRI][hapmap]
rs9637481	0.89[YRI][hapmap]
rs9682444	0.93[YRI][hapmap]
rs9755490	0.93[YRI][hapmap]
rs9835307	0.93[YRI][hapmap]
rs9848268	0.86[EUR][1000 genomes]
rs9859473	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs9860187	0.82[YRI][hapmap]
rs9864243	0.80[EUR][1000 genomes]
rs9873227	0.98[EUR][1000 genomes]
rs9876848	0.93[YRI][hapmap]
rs9879978	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9882443	1.00[CEU][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs9884022	0.81[YRI][hapmap]
rs990211	0.82[CEU][hapmap]

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	nsv590247	chr3:48661985-48801929	Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	esv3407876	chr3:48774454-48823998	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:35)

SNP	Gene	Cis/trans	Tissue	Source
rs6796790	AMT	cis	parietal	SCAN
rs6796790	NICN1	cis	parietal	SCAN
rs6796790	WDR6	cis	Nerve Tibial	GTEx
rs6796790	NCKIPSD	cis	parietal	SCAN
rs6796790	QRICH1	cis	cerebellum	SCAN
rs6796790	NICN1	cis	Thyroid	GTEx
rs6796790	WDR6	cis	lung	GTEx
rs6796790	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs6796790	WDR6	cis	Heart Left Ventricle	GTEx
rs6796790	AMT	cis	Whole Blood	GTEx
rs6796790	P4HTM	cis	parietal	SCAN
rs6796790	NCKIPSD	cis	Nerve Tibial	GTEx
rs6796790	AMT	cis	Nerve Tibial	GTEx
rs6796790	AMT	cis	Adipose Subcutaneous	GTEx
rs6796790	DALRD3	cis	cerebellum	SCAN
rs6796790	LZTFL1	cis	cerebellum	SCAN
rs6796790	AMT	cis	lymphoblastoid	seeQTL
rs6796790	ARIH2	Cis_1M	lymphoblastoid	RTeQTL
rs6796790	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs6796790	ZNF589	cis	parietal	SCAN
rs6796790	QRICH1	cis	Nerve Tibial	GTEx
rs6796790	WDR6	cis	Muscle Skeletal	GTEx
rs6796790	AMT	cis	lung	GTEx
rs6796790	IQCF1	cis	cerebellum	SCAN
rs6796790	AMT	cis	Thyroid	GTEx
rs6796790	WDR6	cis	parietal	SCAN
rs6796790	NICN1-AS1	cis	Thyroid	GTEx
rs6796790	GPX1	cis	parietal	SCAN
rs6796790	DALRD3	cis	parietal	SCAN
rs6796790	TLR9	cis	parietal	SCAN
rs6796790	WDR6	cis	cerebellum	SCAN
rs6796790	AMT	cis	Artery Tibial	GTEx
rs6796790	NICN1	cis	cerebellum	SCAN
rs6796790	PHF7	cis	parietal	SCAN
rs6796790	AMT	cis	cerebellum	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48776200-48783200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:48776200-48784800	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr3:48777400-48782600	Weak transcription	Aorta	Aorta
4	chr3:48777600-48787800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:48777800-48782600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr3:48777800-48783000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:48777800-48783200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr3:48777800-48783400	Weak transcription	Primary B cells from cord blood	blood
9	chr3:48777800-48784000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr3:48777800-48784400	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr3:48777800-48784800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr3:48777800-48784800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr3:48777800-48784800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr3:48777800-48785000	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr3:48777800-48785400	Weak transcription	Primary B cells from peripheral blood	blood
16	chr3:48777800-48785800	Weak transcription	Spleen	Spleen
17	chr3:48777800-48788000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr3:48777800-48788800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:48777800-48807400	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:48778000-48781200	Enhancers	K562	blood
21	chr3:48778000-48783200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr3:48778000-48788000	Weak transcription	HUVEC	blood vessel
23	chr3:48778000-48788200	Weak transcription	NH-A	brain
24	chr3:48778000-48788400	Weak transcription	GM12878-XiMat	blood
25	chr3:48778000-48789000	Weak transcription	NHEK	skin
26	chr3:48778000-48807200	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr3:48778200-48780400	Enhancers	Adipose Nuclei	Adipose
28	chr3:48778200-48782600	Weak transcription	Fetal Intestine Small	intestine
29	chr3:48778200-48782800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:48778200-48782800	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr3:48778200-48783000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr3:48778200-48783000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:48778200-48783000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr3:48778200-48783000	Weak transcription	Lung	lung
35	chr3:48778200-48783200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr3:48778200-48783200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:48778200-48783200	Weak transcription	HSMM	muscle
38	chr3:48778200-48783400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr3:48778200-48783400	Weak transcription	Psoas Muscle	Psoas
40	chr3:48778200-48783800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:48778200-48784400	Weak transcription	Osteobl	bone
42	chr3:48778200-48784600	Weak transcription	Rectal Smooth Muscle	rectum
43	chr3:48778200-48784600	Weak transcription	HMEC	breast
44	chr3:48778200-48784600	Weak transcription	NHDF-Ad	bronchial
45	chr3:48778200-48784800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr3:48778200-48784800	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr3:48778200-48785000	Weak transcription	NHLF	lung
48	chr3:48778200-48785800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr3:48778200-48787800	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr3:48778200-48788400	Weak transcription	Fetal Brain Male	brain

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