Variant report

Variant	rs3796214
Chromosome Location	chr3:69157099-69157100
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

Variant related genes	Relation type
ENSG00000144744	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10489	0.93[GIH][hapmap]
rs1051901	1.00[CEU][hapmap];0.84[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1131960	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12054346	1.00[CEU][hapmap];0.80[JPT][hapmap];1.00[EUR][1000 genomes]
rs17005366	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3772980	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs3772983	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796213	0.84[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap]
rs3821564	1.00[EUR][1000 genomes]
rs4525874	0.81[GIH][hapmap];1.00[MEX][hapmap]
rs56152276	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56194306	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56280964	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57159802	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58277851	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59090383	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60474520	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61086164	0.98[ASN][1000 genomes]
rs6549184	0.89[GIH][hapmap]
rs72924853	1.00[EUR][1000 genomes]
rs72924854	1.00[EUR][1000 genomes]
rs73835715	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs73835716	0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs73835722	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73835726	1.00[EUR][1000 genomes]
rs73835727	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73835728	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73835729	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7617775	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7621394	1.00[EUR][1000 genomes]
rs7621929	1.00[EUR][1000 genomes]
rs937863	0.82[CHB][hapmap];0.85[GIH][hapmap]
rs9843043	0.82[CHB][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

No data

Chromatin state (count:88 , 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	chr3:69155400-69157200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr3:69155400-69157400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr3:69155400-69157600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr3:69155400-69158000	Weak transcription	Brain Substantia Nigra	brain
42	chr3:69155400-69158800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr3:69155400-69159800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr3:69155400-69159800	Weak transcription	Fetal Thymus	thymus
45	chr3:69155400-69160400	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr3:69155400-69164800	Weak transcription	NH-A	brain
47	chr3:69155400-69165800	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr3:69155600-69157400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr3:69155600-69157400	Weak transcription	GM12878-XiMat	blood
50	chr3:69155600-69157600	Weak transcription	Primary neutrophils fromperipheralblood	blood

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