Variant report

Variant	rs12611974
Chromosome Location	chr2:20187671-20187672
allele	A/G
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	SPI1	chr2:20187490-20188192	GM12878	blood:	n/a	n/a
2	RUNX3	chr2:20187643-20188032	GM12878	blood:	n/a	n/a
3	SPI1	chr2:20187654-20188122	GM12891	blood:	n/a	n/a
4	ZNF384	chr2:20187445-20187994	GM12878	blood:	n/a	n/a
5	MXI1	chr2:20187611-20190928	SK-N-SH	brain:	n/a	chr2:20189876-20189891 chr2:20189874-20189889

No.	Distal block	Cell Line	Cell type
1	chr2:20100581..20103342-chr2:20187181..20189808,2	K562	blood:
2	chr2:20187189..20189541-chr2:20212582..20214933,2	K562	blood:
3	chr2:20100581..20103350-chr2:20187181..20189808,3	K562	blood:
4	chr2:20187273..20189318-chr2:20295101..20297253,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000227210	TF binding region
ENSG00000183891	Chromatin interaction
ENSG00000271991	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1030900	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12614643	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12622939	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16987211	0.85[EUR][1000 genomes]
rs16987218	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16987282	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2293670	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3731664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3731665	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3795965	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55919320	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006404	chr2:20167688-20216509	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1005431	chr2:20174676-20210163	Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1011244	chr2:20174676-20216204	Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20117600-20188400	Weak transcription	Brain Angular Gyrus	brain
2	chr2:20128400-20188400	Weak transcription	Colon Smooth Muscle	Colon
3	chr2:20128400-20189200	Weak transcription	Small Intestine	intestine
4	chr2:20129600-20189000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr2:20130200-20189000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr2:20130400-20188800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:20130600-20188800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:20131800-20189000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr2:20136800-20188800	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr2:20136800-20189000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr2:20138200-20188800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr2:20145200-20188000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr2:20162400-20188200	Weak transcription	Brain Substantia Nigra	brain
14	chr2:20163200-20188800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr2:20164200-20187800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr2:20164600-20189000	Weak transcription	Placenta	Placenta
17	chr2:20164800-20189000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr2:20165000-20188400	Weak transcription	K562	blood
19	chr2:20165800-20188200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr2:20169000-20188800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr2:20169000-20189000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr2:20169200-20188800	Weak transcription	Right Ventricle	heart
23	chr2:20171800-20187800	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr2:20172000-20188800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr2:20174000-20188800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr2:20174000-20189000	Weak transcription	Fetal Intestine Small	intestine
27	chr2:20174200-20189400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr2:20174400-20188800	Weak transcription	Fetal Stomach	stomach
29	chr2:20174400-20189200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:20174800-20189200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr2:20175200-20188800	Weak transcription	Adipose Nuclei	Adipose
32	chr2:20175200-20188800	Weak transcription	Liver	Liver
33	chr2:20175800-20188800	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr2:20177000-20188000	Weak transcription	Thymus	Thymus
35	chr2:20177200-20188800	Weak transcription	HSMMtube	muscle
36	chr2:20177800-20187800	Weak transcription	Brain Anterior Caudate	brain
37	chr2:20177800-20187800	Weak transcription	Fetal Brain Female	brain
38	chr2:20177800-20188200	Weak transcription	Brain Germinal Matrix	brain
39	chr2:20177800-20188200	Weak transcription	Fetal Brain Male	brain
40	chr2:20177800-20188400	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr2:20177800-20188800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr2:20177800-20189000	Weak transcription	Primary hematopoietic stem cells	blood
43	chr2:20178000-20187800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr2:20178000-20187800	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr2:20178000-20187800	Weak transcription	HMEC	breast
46	chr2:20178000-20188000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr2:20178000-20188600	Weak transcription	Rectal Smooth Muscle	rectum
48	chr2:20178000-20188800	Weak transcription	Primary T cells from cord blood	blood
49	chr2:20178000-20188800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr2:20178000-20188800	Weak transcription	Duodenum Mucosa	Duodenum

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