Variant report

Variant	rs1863873
Chromosome Location	chr12:9807634-9807635
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:9807468-9807662	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr12:9807303-9807644	K562	blood:	n/a	n/a
3	POLR2A	chr12:9807217-9807726	GM12892	blood:	n/a	n/a
4	POLR2A	chr12:9807302-9808311	HL-60	blood:	n/a	n/a
5	POLR2A	chr12:9806957-9808559	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:9798786..9803516-chr12:9803864..9807970,10	MCF-7	breast:
2	chr12:9807372..9810375-chr12:9810947..9813641,3	K562	blood:
3	chr12:9807372..9809354-chr12:9811080..9813636,2	K562	blood:
4	chr12:9799323..9802837-chr12:9803671..9808302,9	K562	blood:
5	chr12:9807121..9809524-chr12:9821740..9823295,2	K562	blood:
6	chr12:9802928..9804462-chr12:9806298..9808980,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000257027	TF binding region
ENSG00000069493	Chromatin interaction
ENSG00000256442	Chromatin interaction
ENSG00000257027	Chromatin interaction
ENSG00000256594	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10047657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10743806	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10771987	0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10772001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10772010	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10844269	0.83[EUR][1000 genomes]
rs10844325	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844373	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1560007	0.91[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs17805558	0.87[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs1863874	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2401385	0.86[CEU][hapmap]
rs2401386	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs34383380	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764023	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3764024	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7131784	0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7132715	0.83[EUR][1000 genomes]
rs7299076	0.92[ASN][1000 genomes]
rs7313927	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7316121	0.94[ASN][1000 genomes]
rs7959272	0.87[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs7975716	0.87[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs969367	0.88[CHB][hapmap];0.96[JPT][hapmap];0.92[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	nsv427903	chr12:9371593-9830668	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
4	esv1821732	chr12:9560087-9830668	Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv1823760	chr12:9560087-9830668	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv428271	chr12:9560087-9830668	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	esv2757489	chr12:9583455-9810764	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv917178	chr12:9637315-9820153	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9801600-9811200	Weak transcription	Gastric	stomach
2	chr12:9801600-9815600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:9802200-9815200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr12:9802400-9849800	Weak transcription	Pancreas	Pancrea
5	chr12:9802600-9812800	Weak transcription	Ovary	ovary
6	chr12:9802600-9814400	Weak transcription	Colon Smooth Muscle	Colon
7	chr12:9803000-9811200	Weak transcription	Fetal Intestine Small	intestine
8	chr12:9803000-9812200	Weak transcription	Stomach Smooth Muscle	stomach
9	chr12:9803000-9816400	Weak transcription	Brain Germinal Matrix	brain
10	chr12:9803000-9816800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr12:9803000-9819800	Weak transcription	Fetal Brain Female	brain
12	chr12:9803000-9820200	Weak transcription	Brain Substantia Nigra	brain
13	chr12:9803000-9822200	Weak transcription	Small Intestine	intestine
14	chr12:9803200-9812400	Weak transcription	Liver	Liver
15	chr12:9803200-9813400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr12:9803600-9812200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr12:9803600-9826200	Weak transcription	Esophagus	oesophagus
18	chr12:9804000-9814200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr12:9804200-9807800	Weak transcription	Aorta	Aorta
20	chr12:9804200-9811200	Weak transcription	Right Ventricle	heart
21	chr12:9804200-9812400	Weak transcription	Brain Anterior Caudate	brain
22	chr12:9804200-9813200	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr12:9804200-9814200	Weak transcription	Colonic Mucosa	Colon
24	chr12:9804200-9814600	Weak transcription	Lung	lung
25	chr12:9804200-9815000	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr12:9804400-9809400	Weak transcription	Brain Hippocampus Middle	brain
27	chr12:9804400-9810800	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr12:9804400-9811200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr12:9804400-9811200	Weak transcription	Fetal Stomach	stomach
30	chr12:9804400-9811200	Weak transcription	Spleen	Spleen
31	chr12:9804400-9812200	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr12:9804400-9812200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr12:9804400-9812200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:9804400-9814600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr12:9804400-9820400	Weak transcription	HUVEC	blood vessel
36	chr12:9804600-9820000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr12:9804600-9820000	Weak transcription	HMEC	breast
38	chr12:9804600-9820200	Weak transcription	NHEK	skin
39	chr12:9804800-9811200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr12:9805000-9813800	Weak transcription	K562	blood
41	chr12:9805600-9813600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
42	chr12:9805600-9815000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr12:9805600-9819400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr12:9805800-9818200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr12:9806000-9808000	Transcr. at gene 5' and 3'	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr12:9806000-9808000	Strong transcription	Fetal Heart	heart
47	chr12:9806000-9808200	Genic enhancers	Primary B cells from cord blood	blood
48	chr12:9806000-9809800	Genic enhancers	Primary B cells from peripheral blood	blood
49	chr12:9806000-9810400	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
50	chr12:9806000-9813400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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