Variant report

Variant	rs13424841
Chromosome Location	chr2:48335886-48335887
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:48335435..48337113-chr2:48675018..48677889,2	K562	blood:
2	chr2:48333955..48336351-chr2:48337662..48339382,2	K562	blood:
3	chr2:48334951..48336602-chr2:48540623..48542295,2	MCF-7	breast:
4	chr2:48334851..48336463-chr2:48336834..48339382,2	K562	blood:

Variant related genes	Relation type
ENSG00000170802	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10164456	1.00[AMR][1000 genomes]
rs10168301	1.00[AMR][1000 genomes]
rs10169977	1.00[AMR][1000 genomes]
rs10170181	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10171243	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10180159	1.00[AMR][1000 genomes]
rs10180254	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10186155	1.00[AMR][1000 genomes]
rs10187019	1.00[AMR][1000 genomes]
rs10187502	1.00[AMR][1000 genomes]
rs10192404	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10198245	1.00[AMR][1000 genomes]
rs10199615	1.00[AMR][1000 genomes]
rs10209432	1.00[AMR][1000 genomes]
rs13387285	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13387357	1.00[AMR][1000 genomes]
rs13390201	1.00[AMR][1000 genomes]
rs13391880	1.00[AMR][1000 genomes]
rs13397110	1.00[AMR][1000 genomes]
rs13397541	1.00[AMR][1000 genomes]
rs13408320	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13419687	1.00[AMR][1000 genomes]
rs13422341	1.00[AMR][1000 genomes]
rs13430424	1.00[AMR][1000 genomes]
rs7340280	1.00[AMR][1000 genomes]
rs7355330	1.00[AMR][1000 genomes]
rs7355518	1.00[AMR][1000 genomes]
rs9653522	1.00[AMR][1000 genomes]
rs9653523	1.00[AMR][1000 genomes]
rs9653524	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009769	chr2:47972642-48509765	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv535680	chr2:47972642-48509765	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS 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	36 gene(s)	inside rSNPs	diseases
3	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv519831	chr2:48072855-48566031	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv1003766	chr2:48102244-48559654	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv1000455	chr2:48202161-48362638	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv581773	chr2:48277490-48443109	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48333200-48338200	Enhancers	HMEC	breast
2	chr2:48333600-48338200	Weak transcription	Gastric	stomach
3	chr2:48333800-48338200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr2:48333800-48338200	Weak transcription	Stomach Mucosa	stomach
5	chr2:48333800-48338400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr2:48333800-48338400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr2:48333800-48338400	Weak transcription	Ovary	ovary
8	chr2:48334000-48338200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr2:48334000-48338200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr2:48334000-48338200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr2:48334200-48337200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr2:48334200-48337600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr2:48334200-48337800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr2:48334200-48338200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr2:48334200-48338200	Weak transcription	Primary B cells from cord blood	blood
16	chr2:48334200-48338200	Weak transcription	Primary B cells from peripheral blood	blood
17	chr2:48334200-48338200	Weak transcription	Primary T cells from cord blood	blood
18	chr2:48334200-48338200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr2:48334200-48338200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr2:48334200-48338200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr2:48334200-48338200	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr2:48334400-48336800	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr2:48334400-48337200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:48334400-48337200	Weak transcription	Fetal Intestine Large	intestine
25	chr2:48334400-48337200	Weak transcription	Fetal Intestine Small	intestine
26	chr2:48334400-48337800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr2:48334400-48337800	Weak transcription	Brain Substantia Nigra	brain
28	chr2:48334400-48338000	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr2:48334400-48338000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr2:48334400-48338000	Weak transcription	Brain Germinal Matrix	brain
31	chr2:48334400-48338000	Weak transcription	Fetal Brain Female	brain
32	chr2:48334400-48338000	Weak transcription	Fetal Kidney	kidney
33	chr2:48334400-48338000	Weak transcription	Dnd41	blood
34	chr2:48334400-48338200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr2:48334400-48338200	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr2:48334400-48338200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr2:48334400-48338200	Weak transcription	Colonic Mucosa	Colon
38	chr2:48334400-48338200	Weak transcription	Colon Smooth Muscle	Colon
39	chr2:48334400-48338200	Weak transcription	Fetal Stomach	stomach
40	chr2:48334400-48338200	Weak transcription	Fetal Thymus	thymus
41	chr2:48334400-48338200	Weak transcription	Pancreas	Pancrea
42	chr2:48334400-48338200	Weak transcription	Psoas Muscle	Psoas
43	chr2:48334400-48338200	Weak transcription	GM12878-XiMat	blood
44	chr2:48334400-48338400	Weak transcription	Fetal Brain Male	brain
45	chr2:48334600-48337800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:48334600-48337800	Weak transcription	Brain Anterior Caudate	brain
47	chr2:48334600-48338000	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr2:48334600-48338200	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr2:48334600-48338200	Weak transcription	Liver	Liver
50	chr2:48334600-48338200	Weak transcription	Brain Angular Gyrus	brain

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