Variant report

Variant	rs12643903
Chromosome Location	chr4:3321694-3321695
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:3316926..3319273-chr4:3321348..3323892,2	K562	blood:
2	chr4:3321370..3323027-chr4:3448401..3450005,2	MCF-7	breast:
3	chr4:3320336..3322310-chr4:3333644..3335356,2	MCF-7	breast:
4	chr4:3320217..3323147-chr4:3474744..3477107,2	MCF-7	breast:
5	chr4:3299099..3300843-chr4:3320328..3323004,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159788	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12640186	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12640526	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12640721	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs16844197	0.95[CHB][hapmap];0.89[ASN][1000 genomes]
rs16844201	0.95[ASN][1000 genomes]
rs2073286	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2281470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2343799	0.89[ASN][1000 genomes]
rs2749775	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2749776	0.96[ASN][1000 genomes]
rs2749779	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2749786	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2857859	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2857860	0.94[ASN][1000 genomes]
rs3129329	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3129330	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3129331	0.83[ASN][1000 genomes]
rs3129332	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3129333	0.91[ASN][1000 genomes]
rs3129336	0.93[ASN][1000 genomes]
rs58949283	0.90[ASN][1000 genomes]
rs62274923	0.95[ASN][1000 genomes]
rs62274924	0.92[ASN][1000 genomes]
rs73193354	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73193357	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73193371	0.92[ASN][1000 genomes]
rs73193372	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs881818	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv998290	chr4:3176454-3355758	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv878455	chr4:3215835-3344891	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv878456	chr4:3215835-3467519	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv428106	chr4:3226182-3752322	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv878461	chr4:3270488-3339038	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv593440	chr4:3283422-3339038	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv461165	chr4:3283422-3342137	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv593441	chr4:3283422-3342137	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	nsv878462	chr4:3311548-3505448	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
12	nsv1007847	chr4:3317904-3527357	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
13	nsv537001	chr4:3317904-3527357	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3301200-3350000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr4:3307200-3327000	Weak transcription	Fetal Kidney	kidney
3	chr4:3307400-3325600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr4:3307400-3326800	Weak transcription	A549	lung
5	chr4:3307600-3322200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr4:3307600-3323000	Weak transcription	NH-A	brain
7	chr4:3307600-3323600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr4:3308000-3322800	Weak transcription	NHDF-Ad	bronchial
9	chr4:3308000-3323600	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr4:3308000-3323800	Weak transcription	Osteobl	bone
11	chr4:3308000-3326000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr4:3308000-3327000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr4:3308200-3323200	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr4:3308600-3322600	Weak transcription	Brain Substantia Nigra	brain
15	chr4:3308600-3323000	Weak transcription	Brain Angular Gyrus	brain
16	chr4:3309000-3322000	Weak transcription	Right Atrium	heart
17	chr4:3309000-3327200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr4:3314200-3322200	Strong transcription	Fetal Stomach	stomach
19	chr4:3314200-3326600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr4:3314400-3327400	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr4:3314400-3328000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr4:3314400-3348200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr4:3315000-3322400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr4:3315400-3326600	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr4:3315600-3322800	Weak transcription	Dnd41	blood
26	chr4:3316200-3322000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr4:3316600-3322000	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr4:3317800-3321800	Strong transcription	Stomach Smooth Muscle	stomach
29	chr4:3318800-3323000	Weak transcription	HSMMtube	muscle
30	chr4:3319200-3322400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr4:3319200-3332600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr4:3319600-3323800	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr4:3319800-3332000	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr4:3320000-3321800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr4:3320000-3322000	Weak transcription	HUVEC	blood vessel
36	chr4:3320000-3322200	Weak transcription	Brain Anterior Caudate	brain
37	chr4:3320000-3322200	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr4:3320000-3323200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr4:3320000-3323200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr4:3320000-3323200	Weak transcription	Colonic Mucosa	Colon
41	chr4:3320000-3344000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr4:3320200-3322200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr4:3320200-3322400	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr4:3320200-3322600	Weak transcription	Primary T cells from cord blood	blood
45	chr4:3320200-3322600	Weak transcription	Ovary	ovary
46	chr4:3320200-3322800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr4:3320200-3324000	Genic enhancers	Fetal Intestine Small	intestine
48	chr4:3320200-3328400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr4:3320400-3321800	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr4:3320400-3322000	Weak transcription	Brain Cingulate Gyrus	brain

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