Variant report

Variant	rs3796213
Chromosome Location	chr3:69157381-69157382
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:69142493..69145688-chr3:69155509..69158556,4	MCF-7	breast:
2	chr3:69157140..69159067-chr3:69160070..69162293,2	K562	blood:
3	chr3:69127752..69129663-chr3:69155728..69158177,2	K562	blood:

Variant related genes	Relation type
ENSG00000144744	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10489	0.93[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];0.80[ASN][1000 genomes]
rs1051901	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1131960	0.85[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap]
rs12054346	0.81[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs13090606	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs17005366	0.81[CHD][hapmap];1.00[GIH][hapmap]
rs2009602	0.81[CHB][hapmap]
rs2271122	0.81[CHB][hapmap]
rs2292199	0.86[CHB][hapmap]
rs3772979	0.81[CHB][hapmap]
rs3772980	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs3796214	0.84[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap]
rs3821562	0.81[CHB][hapmap]
rs3821564	1.00[ASN][1000 genomes]
rs3853157	0.81[CHB][hapmap]
rs4525874	0.81[GIH][hapmap]
rs60230066	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6549181	0.81[CHB][hapmap]
rs6549184	0.82[CEU][hapmap];0.93[CHB][hapmap];0.89[GIH][hapmap]
rs6777032	0.81[CHB][hapmap]
rs72924853	1.00[ASN][1000 genomes]
rs72924854	1.00[ASN][1000 genomes]
rs73835726	1.00[ASN][1000 genomes]
rs7621394	1.00[ASN][1000 genomes]
rs7621929	1.00[ASN][1000 genomes]
rs7625579	0.93[CHB][hapmap];0.80[ASN][1000 genomes]
rs7627893	0.80[ASN][1000 genomes]
rs7629932	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs937863	0.85[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876933	chr3:69059023-69227379	Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv876934	chr3:69111512-69166895	Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
3	esv2762334	chr3:69157085-69173375	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3796213	CCL3	trans	brain	seeQTL
rs3796213	FABP4	trans	brain	seeQTL
rs3796213	PTGS2	trans	brain	seeQTL
rs3796213	EGR2	trans	brain	seeQTL

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:69142000-69160400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr3:69143600-69160200	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr3:69145600-69160200	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr3:69145800-69160200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:69146200-69160200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:69147400-69160200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:69151200-69157800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr3:69152000-69160200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr3:69153200-69158000	Weak transcription	Psoas Muscle	Psoas
10	chr3:69153600-69160000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:69153800-69160200	Weak transcription	Right Ventricle	heart
12	chr3:69153800-69162400	Weak transcription	HMEC	breast
13	chr3:69153800-69165800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr3:69153800-69168000	Weak transcription	Fetal Muscle Trunk	muscle
15	chr3:69154000-69157400	Weak transcription	Fetal Muscle Leg	muscle
16	chr3:69154000-69157400	Weak transcription	Thymus	Thymus
17	chr3:69154000-69157400	Weak transcription	K562	blood
18	chr3:69154000-69158000	Weak transcription	Brain Anterior Caudate	brain
19	chr3:69154000-69162000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr3:69154000-69162200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr3:69154000-69163200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:69154000-69164800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr3:69154000-69164800	Weak transcription	Right Atrium	heart
24	chr3:69154000-69164800	Weak transcription	NHEK	skin
25	chr3:69154000-69165000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr3:69154000-69165800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr3:69154000-69167800	Weak transcription	Pancreas	Pancrea
28	chr3:69154000-69170200	Weak transcription	Stomach Smooth Muscle	stomach
29	chr3:69154200-69160200	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr3:69154200-69162000	Weak transcription	Brain Angular Gyrus	brain
31	chr3:69154400-69163000	Weak transcription	Fetal Lung	lung
32	chr3:69154400-69166000	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr3:69154600-69160200	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr3:69154800-69157600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr3:69155200-69158000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr3:69155200-69158000	Weak transcription	Placenta	Placenta
37	chr3:69155200-69160000	Weak transcription	Primary B cells from cord blood	blood
38	chr3:69155400-69157400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr3:69155400-69157600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr3:69155400-69158000	Weak transcription	Brain Substantia Nigra	brain
41	chr3:69155400-69158800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr3:69155400-69159800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr3:69155400-69159800	Weak transcription	Fetal Thymus	thymus
44	chr3:69155400-69160400	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr3:69155400-69164800	Weak transcription	NH-A	brain
46	chr3:69155400-69165800	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr3:69155600-69157400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr3:69155600-69157400	Weak transcription	GM12878-XiMat	blood
49	chr3:69155600-69157600	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr3:69155600-69157800	Weak transcription	Primary T cells fromperipheralblood	blood

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