Variant report

Variant	rs28403439
Chromosome Location	chr12:124016104-124016105
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:124016061-124016248	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr12:124014798-124016776	K562	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123955912..123957787-chr12:124014886..124016796,2	K562	blood:
2	chr12:124015709..124018064-chr12:124066858..124069100,3	MCF-7	breast:
3	chr12:123947470..123950375-chr12:124015636..124018854,3	K562	blood:
4	chr12:124006455..124008310-chr12:124016022..124017705,2	K562	blood:
5	chr12:124014934..124016748-chr12:124100287..124103243,2	MCF-7	breast:
6	chr12:123753293..123757508-chr12:124015727..124020202,5	K562	blood:
7	chr12:124015786..124020200-chr12:124020787..124024805,6	K562	blood:
8	chr12:123942564..123944577-chr12:124016063..124019666,4	MCF-7	breast:
9	chr12:123873494..123875550-chr12:124015653..124017169,2	MCF-7	breast:
10	chr12:124014995..124016623-chr12:124054786..124056310,2	MCF-7	breast:

No data

Variant related genes	Relation type
MIR3908	TF binding region
ENSG00000111364	Chromatin interaction
ENSG00000183955	Chromatin interaction
ENSG00000086598	Chromatin interaction
ENSG00000184209	Chromatin interaction
ENSG00000111328	Chromatin interaction
ENSG00000206897	Chromatin interaction
ENSG00000266655	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1057879	1.00[CHB][hapmap];0.82[CHD][hapmap];0.85[ASN][1000 genomes]
rs10773019	1.00[JPT][hapmap]
rs10846526	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10846530	1.00[JPT][hapmap]
rs12308953	1.00[JPT][hapmap]
rs12309685	1.00[JPT][hapmap]
rs12313119	1.00[JPT][hapmap]
rs2048615	0.85[ASN][1000 genomes]
rs2333831	1.00[CHB][hapmap];0.82[CHD][hapmap];0.85[ASN][1000 genomes]
rs28371124	0.85[ASN][1000 genomes]
rs28430750	0.85[ASN][1000 genomes]
rs28454032	0.86[ASN][1000 genomes]
rs28465339	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28478446	0.85[ASN][1000 genomes]
rs28497190	0.85[ASN][1000 genomes]
rs28498381	0.87[EUR][1000 genomes]
rs28535724	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28539789	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28654896	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28673982	0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs28701527	0.85[ASN][1000 genomes]
rs28707421	0.85[ASN][1000 genomes]
rs28711456	0.95[ASN][1000 genomes]
rs28712858	0.85[ASN][1000 genomes]
rs28741988	0.85[ASN][1000 genomes]
rs28758342	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4930716	0.95[ASN][1000 genomes]
rs5027860	0.86[ASN][1000 genomes]
rs59560692	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61953537	0.88[ASN][1000 genomes]
rs61953538	0.90[ASN][1000 genomes]
rs61953539	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61953543	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61953552	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61953557	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71458805	0.81[ASN][1000 genomes]
rs7307227	0.90[ASN][1000 genomes]
rs7313179	0.93[ASN][1000 genomes]
rs7358562	0.82[GIH][hapmap];1.00[JPT][hapmap]
rs7965334	0.86[ASN][1000 genomes]
rs9697543	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9697721	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]

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	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1037260	chr12:123956749-124023069	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1050598	chr12:123991646-124214332	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv541623	chr12:123991646-124214332	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
7	esv2422416	chr12:124009676-124085689	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	nsv560495	chr12:124012974-124017461	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123970000-124016400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr12:123994400-124016200	Weak transcription	Primary hematopoietic stem cells	blood
3	chr12:123994600-124016200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr12:123995200-124016400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr12:123999400-124016400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr12:124001000-124016400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr12:124001200-124017400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr12:124001400-124017400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr12:124002000-124016800	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr12:124004600-124016800	Weak transcription	Stomach Mucosa	stomach
11	chr12:124004800-124016600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr12:124005600-124016400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr12:124005600-124016400	Weak transcription	Duodenum Mucosa	Duodenum
14	chr12:124005800-124016400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr12:124005800-124016600	Weak transcription	Fetal Kidney	kidney
16	chr12:124006200-124017600	Weak transcription	Small Intestine	intestine
17	chr12:124006800-124016800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr12:124007200-124016600	Weak transcription	Primary T cells from cord blood	blood
19	chr12:124007800-124016400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr12:124007800-124016600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr12:124007800-124017000	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr12:124007800-124017400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:124008000-124016400	Weak transcription	Dnd41	blood
24	chr12:124008000-124017000	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr12:124008000-124017400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr12:124008200-124016600	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr12:124008200-124017200	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr12:124008400-124016600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr12:124008400-124017400	Weak transcription	Gastric	stomach
30	chr12:124009200-124016400	Weak transcription	Liver	Liver
31	chr12:124009200-124016400	Weak transcription	Colonic Mucosa	Colon
32	chr12:124009200-124016400	Weak transcription	Fetal Intestine Large	intestine
33	chr12:124009200-124016600	Weak transcription	Lung	lung
34	chr12:124009200-124016600	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr12:124009400-124016600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr12:124010800-124016200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr12:124011000-124016600	Strong transcription	Fetal Intestine Small	intestine
38	chr12:124011400-124016200	Weak transcription	NH-A	brain
39	chr12:124012000-124016600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:124013000-124016600	Weak transcription	HSMMtube	muscle
41	chr12:124014000-124016400	Weak transcription	Spleen	Spleen
42	chr12:124014000-124016600	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr12:124014400-124016400	Strong transcription	HSMM	muscle
44	chr12:124014400-124016800	Genic enhancers	Fetal Heart	heart
45	chr12:124014600-124016600	Weak transcription	NHLF	lung
46	chr12:124014800-124016200	Strong transcription	NHEK	skin
47	chr12:124015000-124016200	Genic enhancers	Primary neutrophils fromperipheralblood	blood
48	chr12:124015000-124016400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr12:124015000-124016400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr12:124015000-124016400	Enhancers	Brain Inferior Temporal Lobe	brain

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