Variant report

Variant	rs11904238
Chromosome Location	chr2:55642570-55642571
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55641621..55644231-chr2:55715263..55717892,2	K562	blood:
2	chr2:55641053..55643696-chr2:55844144..55845979,2	K562	blood:
3	chr2:55633136..55639027-chr2:55639441..55643745,9	K562	blood:

Variant related genes	Relation type
ENSG00000138041	Chromatin interaction
ENSG00000272606	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11898619	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11898783	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11904203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11904613	0.80[AFR][1000 genomes]
rs17046915	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56020076	0.97[AFR][1000 genomes]
rs56214821	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6710144	0.81[AFR][1000 genomes]
rs6718645	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6739731	0.83[AFR][1000 genomes]
rs6759310	0.81[EUR][1000 genomes]
rs73938301	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73939645	0.91[AFR][1000 genomes]
rs73939646	0.94[AFR][1000 genomes]
rs73939825	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73939827	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7564072	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7578788	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers 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 miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55542400-55644800	Weak transcription	Primary T cells from cord blood	blood
2	chr2:55579400-55644400	Weak transcription	Primary B cells from cord blood	blood
3	chr2:55591000-55646000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr2:55601800-55644600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:55616800-55642600	Weak transcription	HUVEC	blood vessel
6	chr2:55623200-55644400	Weak transcription	Fetal Kidney	kidney
7	chr2:55624400-55645600	Weak transcription	Ovary	ovary
8	chr2:55628600-55646000	Weak transcription	Esophagus	oesophagus
9	chr2:55630400-55645800	Weak transcription	Primary B cells from peripheral blood	blood
10	chr2:55630600-55644200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr2:55630800-55644800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr2:55630800-55645200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr2:55630800-55645200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr2:55631000-55645400	Weak transcription	Placenta	Placenta
15	chr2:55631200-55642600	Weak transcription	Colon Smooth Muscle	Colon
16	chr2:55631400-55642600	Weak transcription	Right Ventricle	heart
17	chr2:55631800-55645200	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr2:55632000-55644800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr2:55632600-55645800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:55632800-55645800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr2:55633000-55645000	Weak transcription	Liver	Liver
22	chr2:55633000-55645800	Weak transcription	Fetal Intestine Small	intestine
23	chr2:55633000-55645800	Weak transcription	Spleen	Spleen
24	chr2:55633000-55646000	Weak transcription	Lung	lung
25	chr2:55633200-55644800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr2:55636200-55644200	Weak transcription	Fetal Heart	heart
27	chr2:55636400-55642600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:55636600-55643200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr2:55636600-55644000	Weak transcription	HSMMtube	muscle
30	chr2:55636800-55642600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr2:55636800-55642800	Weak transcription	NH-A	brain
32	chr2:55636800-55644000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr2:55636800-55644000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr2:55636800-55644000	Weak transcription	Primary hematopoietic stem cells	blood
35	chr2:55636800-55644400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr2:55636800-55645600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr2:55637400-55644600	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr2:55637400-55645000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr2:55637600-55642600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr2:55637600-55643200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr2:55638600-55644400	Weak transcription	Fetal Intestine Large	intestine
42	chr2:55639600-55643000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr2:55639800-55644000	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr2:55639800-55644400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr2:55639800-55645600	Weak transcription	Aorta	Aorta
46	chr2:55639800-55645800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr2:55640000-55644200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr2:55640000-55645600	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr2:55640200-55642600	Weak transcription	GM12878-XiMat	blood
50	chr2:55640200-55645800	Weak transcription	Left Ventricle	heart

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