Variant report

Variant	rs3804344
Chromosome Location	chr6:107087870-107087871
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr6:107087842-107088043	HepG2	liver:	n/a	n/a
2	SPI1	chr6:107087580-107088046	HL-60	blood:	n/a	n/a
3	SPI1	chr6:107087699-107087985	GM12891	blood:	n/a	n/a
4	SPI1	chr6:107087685-107088013	GM12891	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:107081802..107084758-chr6:107086846..107089181,2	K562	blood:
2	chr6:107075518..107078241-chr6:107085915..107088324,3	K562	blood:
3	chr6:107076542..107079285-chr6:107086696..107089317,2	K562	blood:
4	chr6:107087373..107089185-chr6:107435277..107437076,2	MCF-7	breast:

No data

Variant related genes	Relation type
RPL21P65	TF binding region
ENSG00000178409	Chromatin interaction
ENSG00000130348	Chromatin interaction
ENSG00000130347	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1613722	1.00[JPT][hapmap]
rs1616375	1.00[JPT][hapmap]
rs1676008	1.00[JPT][hapmap]
rs1676010	1.00[JPT][hapmap]
rs1676025	1.00[JPT][hapmap]
rs1676028	1.00[JPT][hapmap]
rs17067603	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs17506892	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17565194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1770718	1.00[JPT][hapmap]
rs1770721	1.00[JPT][hapmap]
rs1770722	1.00[JPT][hapmap]
rs1770733	1.00[JPT][hapmap]
rs1799693	0.81[TSI][hapmap]
rs2247335	1.00[JPT][hapmap]
rs36016898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3747789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs4946762	1.00[GIH][hapmap];0.82[JPT][hapmap];0.90[TSI][hapmap]
rs57273146	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58328278	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60992370	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66665063	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66991204	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67667413	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6902745	1.00[JPT][hapmap]
rs6903818	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911321	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6925169	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72945076	0.92[EUR][1000 genomes]
rs72946518	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72946522	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72946537	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73509819	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7750387	0.90[EUR][1000 genomes]
rs7771502	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9386565	1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][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	nsv532047	chr6:106591482-107143252	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:107078000-107090000	Weak transcription	Aorta	Aorta
2	chr6:107078400-107090400	Weak transcription	HSMMtube	muscle
3	chr6:107078600-107088000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:107078600-107088000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr6:107078600-107088200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:107078600-107089000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr6:107078600-107089000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr6:107078600-107089400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr6:107078600-107089600	Weak transcription	Fetal Intestine Small	intestine
10	chr6:107078600-107089800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr6:107078600-107090000	Weak transcription	Fetal Muscle Trunk	muscle
12	chr6:107078600-107090000	Weak transcription	Fetal Muscle Leg	muscle
13	chr6:107078600-107090000	Weak transcription	Fetal Stomach	stomach
14	chr6:107078600-107090000	Weak transcription	Right Ventricle	heart
15	chr6:107078600-107090200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr6:107078600-107090200	Weak transcription	Fetal Intestine Large	intestine
17	chr6:107078600-107090200	Weak transcription	Fetal Lung	lung
18	chr6:107078600-107090200	Weak transcription	Ovary	ovary
19	chr6:107078600-107090400	Weak transcription	Brain Hippocampus Middle	brain
20	chr6:107078600-107090400	Weak transcription	Esophagus	oesophagus
21	chr6:107078600-107090400	Weak transcription	Gastric	stomach
22	chr6:107078600-107090400	Weak transcription	HSMM	muscle
23	chr6:107078600-107090600	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr6:107078600-107090600	Weak transcription	Fetal Brain Female	brain
25	chr6:107078600-107092000	Weak transcription	Brain Germinal Matrix	brain
26	chr6:107078600-107092600	Weak transcription	Brain Anterior Caudate	brain
27	chr6:107078600-107093000	Weak transcription	Colonic Mucosa	Colon
28	chr6:107078600-107100200	Weak transcription	Rectal Smooth Muscle	rectum
29	chr6:107078600-107100400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr6:107078600-107103800	Weak transcription	Fetal Brain Male	brain
31	chr6:107078600-107104200	Weak transcription	Brain Angular Gyrus	brain
32	chr6:107078600-107106200	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr6:107078600-107106600	Weak transcription	NH-A	brain
34	chr6:107078600-107110200	Weak transcription	NHLF	lung
35	chr6:107078600-107110800	Weak transcription	Fetal Heart	heart
36	chr6:107078600-107115200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr6:107078600-107125200	Weak transcription	Stomach Mucosa	stomach
38	chr6:107078800-107088000	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr6:107078800-107088200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr6:107078800-107089000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr6:107078800-107089400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr6:107078800-107090200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr6:107078800-107090400	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr6:107078800-107090600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr6:107078800-107090600	Weak transcription	Hela-S3	cervix
46	chr6:107078800-107092000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr6:107078800-107093600	Weak transcription	NHEK	skin
48	chr6:107079400-107091000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr6:107079400-107092600	Weak transcription	HMEC	breast
50	chr6:107079400-107092800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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