Variant report

Variant	rs13412171
Chromosome Location	chr2:38879950-38879951
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38827420..38830831-chr2:38879840..38883102,4	K562	blood:
2	chr2:38879772..38882593-chr2:38978947..38981476,2	K562	blood:
3	chr2:38879814..38882586-chr2:38892083..38894543,4	K562	blood:

Variant related genes	Relation type
ENSG00000143889	Chromatin interaction
ENSG00000235586	Chromatin interaction
ENSG00000143891	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs13032371	0.84[ASN][1000 genomes]
rs13393767	0.88[AFR][1000 genomes]
rs13421362	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13432435	0.80[ASN][1000 genomes]
rs17022996	0.81[CHB][hapmap]
rs17023003	0.86[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2099261	0.85[ASN][1000 genomes]
rs2217537	0.80[ASN][1000 genomes]
rs2373421	0.81[CHB][hapmap]
rs6544169	0.81[CHB][hapmap];0.81[CHD][hapmap]
rs6544171	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6717958	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6733950	0.86[CEU][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];0.81[TSI][hapmap];0.85[ASN][1000 genomes]
rs6735134	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6745646	0.80[ASN][1000 genomes]
rs6751018	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7562949	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7566698	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs891706	0.92[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	nsv581485	chr2:38839323-38893660	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv873882	chr2:38858669-38921498	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv2762495	chr2:38861095-38886391	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	esv3457549	chr2:38871768-38882574	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	esv3457553	chr2:38871805-38882546	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	esv3457551	chr2:38871805-38882561	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	esv3457550	chr2:38871849-38882546	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	esv14023	chr2:38871950-38882521	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	esv2421758	chr2:38873799-38881106	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
12	esv2760617	chr2:38873799-38886391	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	nsv516043	chr2:38874177-38881106	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
14	nsv817740	chr2:38874177-38881106	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38870800-38881600	Weak transcription	Spleen	Spleen
2	chr2:38871200-38880800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr2:38874600-38880800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr2:38875600-38880600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr2:38875800-38880600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:38875800-38880800	Weak transcription	HMEC	breast
7	chr2:38876000-38882000	Weak transcription	Thymus	Thymus
8	chr2:38876600-38880400	Weak transcription	Dnd41	blood
9	chr2:38877200-38882000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr2:38877200-38882200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr2:38877800-38880000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr2:38878200-38880800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr2:38878200-38888400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr2:38878400-38880000	Enhancers	Primary hematopoietic stem cells	blood
15	chr2:38878400-38882000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr2:38878600-38883000	Enhancers	Primary T cells fromperipheralblood	blood
17	chr2:38878800-38881600	Enhancers	Stomach Mucosa	stomach
18	chr2:38879000-38880600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr2:38879000-38881200	Enhancers	Duodenum Mucosa	Duodenum
20	chr2:38879000-38882000	Enhancers	Placenta	Placenta
21	chr2:38879000-38882800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr2:38879200-38880400	Enhancers	Primary B cells from peripheral blood	blood
23	chr2:38879200-38880400	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr2:38879200-38880600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr2:38879200-38882800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr2:38879400-38880400	Enhancers	Small Intestine	intestine
27	chr2:38879400-38881400	Enhancers	Monocytes-CD14+_RO01746	blood
28	chr2:38879400-38882200	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr2:38879400-38882200	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr2:38879400-38883000	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr2:38879400-38883000	Enhancers	Fetal Thymus	thymus
32	chr2:38879600-38880200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr2:38879600-38880200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
34	chr2:38879600-38880200	Flanking Active TSS	K562	blood
35	chr2:38879600-38880400	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr2:38879600-38880600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr2:38879600-38880600	Enhancers	HepG2	liver
38	chr2:38879600-38881600	Enhancers	Hela-S3	cervix
39	chr2:38879600-38882000	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr2:38879800-38880000	Enhancers	GM12878-XiMat	blood

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