Variant report

Variant	rs2274408
Chromosome Location	chr13:95859974-95859975
allele	C/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	PAX5	chr13:95859932-95860668	GM12878	blood:	n/a	n/a
2	FOXM1	chr13:95859965-95860660	GM12878	blood:	n/a	n/a
3	NFIC	chr13:95859890-95860718	GM12878	blood:	n/a	n/a
4	GATA1	chr13:95859914-95860610	K562	blood:	n/a	chr13:95860228-95860237 chr13:95860229-95860246
5	EP300	chr13:95859753-95861073	SK-N-SH	brain:	n/a	chr13:95859814-95859828
6	MXI1	chr13:95859872-95860997	SK-N-SH	brain:	n/a	n/a
7	EP300	chr13:95859967-95860823	GM12878	blood:	n/a	n/a
8	GATA1	chr13:95859967-95860291	PBDEFetal	blood:	n/a	chr13:95860228-95860237 chr13:95860229-95860246

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:95858681..95860676-chr13:95871438..95873483,2	K562	blood:

Variant related genes	Relation type
ENSG00000238463	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1815344	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2013713	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2274405	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2274406	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2274410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2389204	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3818486	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3818493	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3818494	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3818495	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4773845	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4773846	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7331142	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7983079	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9516536	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9524827	0.96[CEU][hapmap];0.90[CHB][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9590200	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][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	nsv533659	chr13:95757713-96042149	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv832689	chr13:95759073-95921308	Genic enhancers ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:95807200-95865600	Weak transcription	Colonic Mucosa	Colon
2	chr13:95827400-95872400	Weak transcription	NH-A	brain
3	chr13:95834000-95865400	Weak transcription	Psoas Muscle	Psoas
4	chr13:95838200-95867400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr13:95839400-95863800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr13:95840400-95874400	Weak transcription	Pancreas	Pancrea
7	chr13:95842000-95864800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr13:95842000-95869000	Weak transcription	Fetal Kidney	kidney
9	chr13:95842200-95898200	Weak transcription	NHDF-Ad	bronchial
10	chr13:95844400-95864400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr13:95844400-95865600	Weak transcription	Spleen	Spleen
12	chr13:95844400-95867600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr13:95844600-95863600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr13:95846000-95871400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr13:95846200-95872400	Weak transcription	Brain Anterior Caudate	brain
16	chr13:95847800-95860200	Weak transcription	Primary B cells from peripheral blood	blood
17	chr13:95847800-95868200	Weak transcription	Fetal Lung	lung
18	chr13:95847800-95880400	Weak transcription	Ovary	ovary
19	chr13:95848400-95861600	Weak transcription	HSMMtube	muscle
20	chr13:95850800-95867600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr13:95852800-95862200	Weak transcription	Right Ventricle	heart
22	chr13:95853800-95863400	Weak transcription	Adipose Nuclei	Adipose
23	chr13:95855000-95863000	Strong transcription	Fetal Intestine Small	intestine
24	chr13:95855200-95862200	Strong transcription	Skeletal Muscle Male	skeletal muscle
25	chr13:95855400-95863400	Weak transcription	Osteobl	bone
26	chr13:95855400-95867400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr13:95855600-95861800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr13:95855800-95862000	Strong transcription	NHLF	lung
29	chr13:95856000-95863000	Strong transcription	A549	lung
30	chr13:95856000-95864400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr13:95856400-95865400	Weak transcription	Left Ventricle	heart
32	chr13:95856400-95872600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr13:95856400-95898200	Weak transcription	NHEK	skin
34	chr13:95857000-95860200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr13:95857200-95860600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr13:95857400-95865400	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr13:95857600-95861400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr13:95857800-95860400	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr13:95857800-95863000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr13:95858200-95865600	Weak transcription	Small Intestine	intestine
41	chr13:95858400-95860400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr13:95858600-95860200	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr13:95858600-95861200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr13:95858600-95865600	Weak transcription	Brain Hippocampus Middle	brain
45	chr13:95858600-95880400	Weak transcription	Fetal Thymus	thymus
46	chr13:95858800-95861400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr13:95858800-95861400	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr13:95858800-95861400	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr13:95858800-95866200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr13:95859000-95860200	Weak transcription	Primary hematopoietic stem cells	blood

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