Variant report

Variant	rs7611413
Chromosome Location	chr3:52106514-52106515
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52091359..52093112-chr3:52104568..52106950,2	K562	blood:
2	chr3:52100511..52102649-chr3:52105549..52107890,2	K562	blood:
3	chr3:52085365..52087890-chr3:52105786..52108458,2	MCF-7	breast:
4	chr3:52104770..52107611-chr3:52108518..52111344,2	K562	blood:
5	chr3:52105087..52107188-chr3:52123209..52125122,2	K562	blood:
6	chr3:52089077..52093112-chr3:52104512..52107618,4	K562	blood:

Variant related genes	Relation type
ENSG00000164086	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1587921	1.00[TSI][hapmap]
rs17052020	1.00[MEX][hapmap]
rs3774344	1.00[MEX][hapmap]
rs6445259	1.00[ASW][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]
rs6784764	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6803639	0.87[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7614535	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7615736	1.00[MEX][hapmap]
rs7618228	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7652969	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7652984	1.00[ASW][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]
rs973948	1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv1804090	chr3:51962081-52140591	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	esv1835339	chr3:51962081-52140591	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
4	nsv1003581	chr3:51973395-52108645	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	nsv1001062	chr3:51973395-52134638	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
7	nsv876786	chr3:52041566-52236762	Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52092200-52107800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:52096000-52107800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:52097400-52110800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:52097600-52108200	Weak transcription	NHLF	lung
5	chr3:52097600-52119800	Weak transcription	GM12878-XiMat	blood
6	chr3:52099400-52107000	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr3:52100000-52108200	Weak transcription	Gastric	stomach
8	chr3:52100200-52106600	Enhancers	Fetal Muscle Trunk	muscle
9	chr3:52101800-52110200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:52102000-52111200	Weak transcription	Fetal Kidney	kidney
11	chr3:52102200-52107600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr3:52102400-52106600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:52102600-52108200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr3:52102600-52121000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr3:52102800-52106600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:52102800-52107600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:52102800-52107600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr3:52102800-52107800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:52103000-52106800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr3:52103000-52107600	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr3:52103200-52108200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr3:52103200-52122000	Weak transcription	Duodenum Mucosa	Duodenum
23	chr3:52103200-52124800	Weak transcription	Colonic Mucosa	Colon
24	chr3:52103400-52107600	Weak transcription	HepG2	liver
25	chr3:52103400-52114600	Weak transcription	Fetal Intestine Large	intestine
26	chr3:52103600-52107400	Weak transcription	Thymus	Thymus
27	chr3:52103600-52108000	Weak transcription	Fetal Intestine Small	intestine
28	chr3:52103800-52107000	Enhancers	Spleen	Spleen
29	chr3:52103800-52107400	Enhancers	Fetal Brain Male	brain
30	chr3:52103800-52107600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr3:52104000-52107200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr3:52104200-52108400	Enhancers	Right Atrium	heart
33	chr3:52104400-52107200	Enhancers	Brain Cingulate Gyrus	brain
34	chr3:52104400-52107200	Enhancers	Fetal Brain Female	brain
35	chr3:52104600-52107000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr3:52105200-52110400	Weak transcription	Aorta	Aorta
37	chr3:52105200-52110400	Weak transcription	Brain Substantia Nigra	brain
38	chr3:52105400-52106600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr3:52105400-52106800	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr3:52105400-52107000	Enhancers	Primary T cells fromperipheralblood	blood
41	chr3:52105600-52106600	Enhancers	Monocytes-CD14+_RO01746	blood
42	chr3:52105600-52106800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr3:52105600-52107400	Weak transcription	Fetal Stomach	stomach
44	chr3:52105600-52107800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr3:52105600-52110400	Weak transcription	Fetal Lung	lung
46	chr3:52105600-52110800	Weak transcription	Colon Smooth Muscle	Colon
47	chr3:52105600-52111200	Weak transcription	Osteobl	bone
48	chr3:52105600-52119600	Weak transcription	Primary hematopoietic stem cells	blood
49	chr3:52105600-52120800	Strong transcription	Dnd41	blood
50	chr3:52105600-52124000	Weak transcription	Pancreas	Pancrea

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