Variant report

Variant	rs2071703
Chromosome Location	chr4:3241413-3241414
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr4:3241360-3241510	GM12865	blood:	n/a	n/a
2	POLR2A	chr4:3241096-3241469	GM12891	blood:	n/a	n/a
3	POLR2A	chr4:3241136-3241451	GM12878	blood:	n/a	n/a
4	POLR2A	chr4:3241257-3241511	Hela-S3	cervix:	n/a	n/a
5	MYC	chr4:3241347-3241431	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr4:3241125-3241551	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:3239414..3242186-chr4:3248483..3251148,2	MCF-7	breast:
2	chr4:3233021..3235441-chr4:3240275..3242127,2	K562	blood:
3	chr4:3236106..3239124-chr4:3240475..3243482,3	K562	blood:
4	chr4:3237753..3241593-chr4:3242889..3245748,3	K562	blood:

Variant related genes	Relation type
MSANTD1	TF binding region
ENSG00000188981	Chromatin interaction
ENSG00000197386	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1547410	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2269499	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2298971	0.83[ASN][1000 genomes]
rs3095075	0.84[ASN][1000 genomes]
rs3121417	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3121418	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3121419	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3129321	0.83[ASN][1000 genomes]
rs3129322	0.86[ASN][1000 genomes]
rs3135175	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34155847	0.87[ASN][1000 genomes]
rs362268	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs362271	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs362272	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs362273	0.82[EUR][1000 genomes]
rs362275	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs362296	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs362306	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs362309	0.95[ASN][1000 genomes]
rs362312	0.91[ASN][1000 genomes]
rs362336	0.85[ASN][1000 genomes]
rs363088	0.83[ASN][1000 genomes]
rs363092	0.83[ASN][1000 genomes]
rs3755883	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3775061	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73193303	0.81[ASN][1000 genomes]
rs82332	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs82334	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv524211	chr4:3215835-3270488	Strong transcription Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv470003	chr4:3215835-3275484	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv878454	chr4:3215835-3305739	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	nsv878457	chr4:3231661-3278517	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
11	nsv878458	chr4:3235518-3303976	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
12	nsv878459	chr4:3235518-3310831	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3114600-3292400	Weak transcription	Right Atrium	heart
2	chr4:3196000-3242600	Strong transcription	Fetal Intestine Small	intestine
3	chr4:3204800-3246000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr4:3206000-3244600	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr4:3206000-3246400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr4:3207600-3243600	Strong transcription	Primary B cells from peripheral blood	blood
7	chr4:3207600-3244000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr4:3207600-3244600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr4:3207600-3245400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr4:3207600-3246400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr4:3207800-3243200	Strong transcription	Sigmoid Colon	Sigmoid Colon
12	chr4:3207800-3243800	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr4:3207800-3244400	Strong transcription	Duodenum Mucosa	Duodenum
14	chr4:3207800-3245400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr4:3208000-3243600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr4:3208200-3246400	Strong transcription	Fetal Thymus	thymus
17	chr4:3208400-3244800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr4:3210000-3244200	Strong transcription	Fetal Intestine Large	intestine
19	chr4:3210000-3245000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr4:3210000-3246600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr4:3210400-3247000	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr4:3211600-3246400	Strong transcription	Thymus	Thymus
23	chr4:3213400-3242600	Strong transcription	Ovary	ovary
24	chr4:3213400-3243400	Strong transcription	Dnd41	blood
25	chr4:3213400-3245600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr4:3213600-3245600	Strong transcription	Placenta Amnion	Placenta Amnion
27	chr4:3213800-3247600	Strong transcription	Primary T cells from cord blood	blood
28	chr4:3214000-3243400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr4:3222600-3241600	Strong transcription	Adipose Nuclei	Adipose
30	chr4:3223200-3243800	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr4:3223400-3247600	Strong transcription	Fetal Brain Female	brain
32	chr4:3228800-3246600	Strong transcription	Liver	Liver
33	chr4:3229000-3243000	Strong transcription	Placenta	Placenta
34	chr4:3229000-3245400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr4:3229200-3243000	Strong transcription	Brain Angular Gyrus	brain
36	chr4:3229600-3242800	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr4:3229600-3244800	Strong transcription	Brain Anterior Caudate	brain
38	chr4:3229800-3242800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr4:3229800-3243800	Strong transcription	Brain Cingulate Gyrus	brain
40	chr4:3229800-3245200	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr4:3229800-3245200	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr4:3230000-3242200	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr4:3230000-3242800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr4:3230000-3245600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr4:3230200-3242000	Strong transcription	Rectal Smooth Muscle	rectum
46	chr4:3230200-3243000	Strong transcription	Aorta	Aorta
47	chr4:3230400-3245600	Strong transcription	Brain Germinal Matrix	brain
48	chr4:3231400-3247400	Strong transcription	Spleen	Spleen
49	chr4:3231600-3243800	Strong transcription	Gastric	stomach
50	chr4:3231600-3244200	Strong transcription	Esophagus	oesophagus

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