Variant report

Variant	rs13420264
Chromosome Location	chr2:190440397-190440398
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:190430886..190434055-chr2:190440352..190443388,4	K562	blood:
2	chr2:190326973..190329897-chr2:190440018..190441617,2	K562	blood:
3	chr2:190307453..190310457-chr2:190438182..190441040,3	K562	blood:
4	chr2:190334143..190336908-chr2:190438147..190441105,2	MCF-7	breast:
5	chr2:190438086..190442028-chr2:190445143..190449183,3	MCF-7	breast:
6	chr2:190437016..190438536-chr2:190439117..190440686,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115368	Chromatin interaction
ENSG00000138449	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10195345	0.92[AFR][1000 genomes]
rs13388478	0.91[AFR][1000 genomes]
rs13398454	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs13399776	0.91[AFR][1000 genomes]
rs13404407	0.85[AFR][1000 genomes]
rs13411677	1.00[AFR][1000 genomes]
rs13419514	0.92[AFR][1000 genomes]
rs13419629	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs13420166	1.00[AFR][1000 genomes]
rs13421111	0.83[AFR][1000 genomes]
rs13426218	1.00[YRI][hapmap]
rs13431938	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs28435467	1.00[AFR][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	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv875615	chr2:190215527-190444392	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190424800-190441800	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr2:190424800-190444400	Weak transcription	Brain Substantia Nigra	brain
3	chr2:190426600-190444200	Weak transcription	Brain Angular Gyrus	brain
4	chr2:190428400-190443800	Weak transcription	Brain Germinal Matrix	brain
5	chr2:190429000-190441600	Weak transcription	Fetal Brain Female	brain
6	chr2:190429000-190442000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:190429000-190444400	Weak transcription	Thymus	Thymus
8	chr2:190429800-190441800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:190430200-190443400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:190430400-190444600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr2:190431200-190444400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:190431600-190441200	Weak transcription	Brain Hippocampus Middle	brain
13	chr2:190432000-190444600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr2:190432600-190441200	Weak transcription	Spleen	Spleen
15	chr2:190434000-190440800	Weak transcription	Primary B cells from cord blood	blood
16	chr2:190434200-190444800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr2:190434400-190441800	Weak transcription	Fetal Stomach	stomach
18	chr2:190434400-190442000	Weak transcription	Brain Anterior Caudate	brain
19	chr2:190434400-190444400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr2:190435400-190441600	Strong transcription	K562	blood
21	chr2:190435800-190440400	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr2:190435800-190441200	Weak transcription	Fetal Muscle Leg	muscle
23	chr2:190435800-190441600	Weak transcription	Right Ventricle	heart
24	chr2:190435800-190443000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr2:190435800-190444400	Weak transcription	NHLF	lung
26	chr2:190436000-190444800	Weak transcription	HSMM	muscle
27	chr2:190436800-190440600	Transcr. at gene 5' and 3'	Ovary	ovary
28	chr2:190436800-190442200	Enhancers	Pancreatic Islets	Pancreatic Islet
29	chr2:190436800-190442800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:190437000-190441200	Genic enhancers	Fetal Intestine Large	intestine
31	chr2:190438200-190441000	Genic enhancers	Primary T cells from cord blood	blood
32	chr2:190438200-190441400	Genic enhancers	Dnd41	blood
33	chr2:190438600-190441600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr2:190438600-190444200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:190438800-190441800	Weak transcription	Fetal Heart	heart
36	chr2:190438800-190443000	Weak transcription	Colon Smooth Muscle	Colon
37	chr2:190438800-190444400	Weak transcription	Fetal Thymus	thymus
38	chr2:190439000-190441200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
39	chr2:190439000-190441800	Active TSS	Right Atrium	heart
40	chr2:190439000-190442200	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr2:190439000-190442200	Enhancers	HepG2	liver
42	chr2:190439200-190444400	Flanking Active TSS	Liver	Liver
43	chr2:190439400-190441000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr2:190439400-190441800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr2:190439600-190440600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr2:190439600-190441600	Enhancers	Colonic Mucosa	Colon
47	chr2:190439600-190441600	Genic enhancers	Fetal Intestine Small	intestine
48	chr2:190439600-190441800	Active TSS	Aorta	Aorta
49	chr2:190439600-190441800	Genic enhancers	Placenta	Placenta
50	chr2:190439600-190442800	Enhancers	Small Intestine	intestine

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