Variant report

Variant	rs6797164
Chromosome Location	chr3:49506299-49506300
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr3:49506252-49509681	SK-N-SH	brain:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49447402..49451449-chr3:49505916..49509646,7	K562	blood:
2	chr3:49447402..49452044-chr3:49506038..49509646,9	K562	blood:
3	chr3:49505441..49508480-chr3:49710122..49713377,5	MCF-7	breast:
4	chr3:49501861..49505109-chr3:49505439..49508808,5	K562	blood:
5	chr3:49448236..49450769-chr3:49505936..49509558,3	MCF-7	breast:
6	chr3:49043383..49045852-chr3:49505855..49507402,2	MCF-7	breast:
7	chr3:49065352..49067075-chr3:49506284..49508355,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DAG1-1	chr3:49506146-49506488	NONHSAT089696

No data

Variant related genes	Relation type
DAG1	TF binding region
RNA5SP130	TF binding region
ENSG00000178252	Chromatin interaction
ENSG00000272434	Chromatin interaction
ENSG00000178035	Chromatin interaction
ENSG00000164062	Chromatin interaction
ENSG00000067560	Chromatin interaction
ENSG00000145022	Chromatin interaction
ENSG00000201301	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11130197	1.00[YRI][hapmap]
rs11708174	1.00[YRI][hapmap]
rs11717485	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1522929	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1568663	1.00[AMR][1000 genomes]
rs17080495	0.88[YRI][hapmap];1.00[AMR][1000 genomes]
rs17080510	0.88[YRI][hapmap];1.00[AMR][1000 genomes]
rs17080567	1.00[AMR][1000 genomes]
rs17080664	0.88[YRI][hapmap]
rs1996874	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2311794	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2311801	0.87[YRI][hapmap]
rs2329024	1.00[YRI][hapmap]
rs3870340	1.00[YRI][hapmap]
rs3912831	1.00[YRI][hapmap]
rs4241409	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4452334	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4855856	1.00[YRI][hapmap]
rs4855857	1.00[YRI][hapmap]
rs4855870	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4855872	0.83[AFR][1000 genomes]
rs4855874	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4855875	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4855876	1.00[AMR][1000 genomes]
rs4855878	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4855879	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs55808753	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55990645	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56101322	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56760510	1.00[AMR][1000 genomes]
rs56897974	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60011446	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61749312	1.00[AMR][1000 genomes]
rs6446269	0.81[AFR][1000 genomes]
rs6446270	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6446271	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6446273	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6446276	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6446278	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs6446279	1.00[AMR][1000 genomes]
rs6762593	1.00[YRI][hapmap]
rs6766297	1.00[AMR][1000 genomes]
rs6787665	1.00[AMR][1000 genomes]
rs6793124	1.00[AMR][1000 genomes]
rs73830703	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73830704	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73830705	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73830706	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7646393	1.00[YRI][hapmap]
rs8179172	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9311441	0.83[AFR][1000 genomes]
rs9830627	1.00[AMR][1000 genomes]
rs9861805	1.00[AMR][1000 genomes]

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	nsv834687	chr3:49448632-49631788	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv3420339	chr3:49505548-49510046	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49490600-49506600	Enhancers	Fetal Muscle Leg	muscle
2	chr3:49497400-49506400	Weak transcription	Brain Germinal Matrix	brain
3	chr3:49499600-49506600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:49500000-49506400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:49500000-49506400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:49500000-49506400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr3:49500000-49506400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr3:49500000-49506400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:49500000-49506400	Weak transcription	Psoas Muscle	Psoas
10	chr3:49500000-49506400	Weak transcription	NH-A	brain
11	chr3:49500000-49506400	Weak transcription	NHDF-Ad	bronchial
12	chr3:49500000-49506600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:49501400-49506600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:49502200-49506600	Enhancers	Fetal Muscle Trunk	muscle
15	chr3:49502400-49506400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:49502600-49506800	Enhancers	Fetal Heart	heart
17	chr3:49503000-49506600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:49503400-49506400	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr3:49503400-49506400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr3:49503400-49506400	Weak transcription	Colonic Mucosa	Colon
21	chr3:49503400-49506400	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr3:49503600-49506400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:49503600-49506400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:49503600-49506400	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr3:49503600-49506400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr3:49503600-49506400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr3:49503600-49506400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:49503600-49506400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:49503600-49506400	Weak transcription	Brain Anterior Caudate	brain
30	chr3:49503600-49506400	Weak transcription	Fetal Intestine Large	intestine
31	chr3:49503600-49506400	Weak transcription	HSMM	muscle
32	chr3:49503600-49506400	Weak transcription	NHEK	skin
33	chr3:49503600-49506600	Weak transcription	Primary hematopoietic stem cells	blood
34	chr3:49503600-49506600	Weak transcription	Brain Angular Gyrus	brain
35	chr3:49503600-49507200	Weak transcription	Spleen	Spleen
36	chr3:49503800-49506400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:49503800-49506400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr3:49503800-49506400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr3:49503800-49506400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr3:49503800-49506400	Weak transcription	Brain Cingulate Gyrus	brain
41	chr3:49503800-49506400	Weak transcription	Brain Hippocampus Middle	brain
42	chr3:49503800-49506400	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr3:49503800-49506400	Weak transcription	Brain Substantia Nigra	brain
44	chr3:49503800-49506400	Weak transcription	Gastric	stomach
45	chr3:49503800-49506400	Weak transcription	Right Atrium	heart
46	chr3:49503800-49506400	Enhancers	HepG2	liver
47	chr3:49503800-49506400	Weak transcription	HMEC	breast
48	chr3:49503800-49506600	Weak transcription	Esophagus	oesophagus
49	chr3:49503800-49506600	Weak transcription	Ovary	ovary
50	chr3:49504000-49506400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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