Variant report

Variant	rs25952
Chromosome Location	chr5:14695247-14695248
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:14664522..14666379-chr5:14695196..14698003,3	K562	blood:
2	chr5:14666421..14668371-chr5:14694301..14697182,2	K562	blood:

Variant related genes	Relation type
ENSG00000261360	Chromatin interaction
ENSG00000154124	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10062487	0.88[EUR][1000 genomes]
rs10078335	0.90[EUR][1000 genomes]
rs13180883	1.00[ASW][hapmap]
rs13189930	0.87[JPT][hapmap]
rs149181	0.83[ASN][1000 genomes]
rs149197	1.00[ASW][hapmap]
rs149493	0.85[ASN][1000 genomes]
rs149617	0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs152788	0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs153829	0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs153830	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs166127	0.89[ASN][1000 genomes]
rs183681	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1875513	1.00[JPT][hapmap]
rs2455402	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs250435	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs250439	0.85[ASN][1000 genomes]
rs250440	0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs250862	0.87[ASN][1000 genomes]
rs251496	0.88[ASN][1000 genomes]
rs258290	0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs258374	0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs25945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs25951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs25961	1.00[ASW][hapmap]
rs25983	0.87[JPT][hapmap]
rs25986	0.91[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs25987	0.91[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs25988	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs25992	1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs26307	0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs27356	0.87[JPT][hapmap]
rs27882	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs27911	1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs31919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs31920	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs31921	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs31922	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs31923	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs31924	0.81[CHB][hapmap];0.82[ASN][1000 genomes]
rs31925	0.83[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs31926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs31928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs31929	1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs31930	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs31968	0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs31974	1.00[ASW][hapmap]
rs3866215	0.85[JPT][hapmap]
rs40578	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs42358	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs42410	0.99[ASN][1000 genomes]
rs42681	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs456180	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs457897	1.00[ASW][hapmap]
rs459467	0.88[ASN][1000 genomes]
rs466880	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4702043	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs6554856	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6872954	1.00[JPT][hapmap]
rs73048831	0.88[EUR][1000 genomes]
rs73048837	0.86[EUR][1000 genomes]
rs73048838	0.82[EUR][1000 genomes]
rs745328	0.93[JPT][hapmap]
rs95492	0.81[CHB][hapmap];0.93[JPT][hapmap];0.94[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	nsv1026914	chr5:14237782-14751588	Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1018187	chr5:14385164-15127103	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs25952	FAM105B	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14674000-14712800	Strong transcription	Fetal Intestine Large	intestine
2	chr5:14674600-14695600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:14675200-14695800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr5:14676800-14705600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr5:14677600-14705600	Strong transcription	Dnd41	blood
6	chr5:14677800-14704000	Strong transcription	HepG2	liver
7	chr5:14678600-14704200	Strong transcription	Fetal Thymus	thymus
8	chr5:14684600-14726200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr5:14686400-14700800	Strong transcription	Primary T cells from cord blood	blood
10	chr5:14686600-14695600	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr5:14686800-14698800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr5:14686800-14699200	Strong transcription	Osteobl	bone
13	chr5:14686800-14704200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr5:14687000-14700200	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr5:14687400-14696600	Strong transcription	HUVEC	blood vessel
16	chr5:14687600-14696600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
17	chr5:14687800-14700400	Strong transcription	HSMM	muscle
18	chr5:14687800-14702800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr5:14688000-14696600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr5:14688000-14698600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
21	chr5:14690600-14700800	Strong transcription	Rectal Mucosa Donor 31	rectum
22	chr5:14690800-14696000	Strong transcription	Primary hematopoietic stem cells	blood
23	chr5:14690800-14696600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr5:14690800-14696800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr5:14690800-14696800	Strong transcription	Liver	Liver
26	chr5:14690800-14696800	Strong transcription	NHEK	skin
27	chr5:14690800-14697200	Strong transcription	Brain Inferior Temporal Lobe	brain
28	chr5:14690800-14697200	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr5:14690800-14699800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr5:14690800-14700000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr5:14690800-14700200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr5:14690800-14700200	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr5:14690800-14700200	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr5:14690800-14700400	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr5:14690800-14700400	Strong transcription	Duodenum Mucosa	Duodenum
36	chr5:14690800-14700400	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr5:14690800-14700400	Strong transcription	HMEC	breast
38	chr5:14690800-14701000	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr5:14690800-14702600	Strong transcription	Primary B cells from cord blood	blood
40	chr5:14690800-14703000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr5:14690800-14704000	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr5:14690800-14706000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr5:14690800-14710600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr5:14690800-14717200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr5:14691000-14695600	Strong transcription	A549	lung
46	chr5:14691000-14696000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr5:14691000-14696600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr5:14691000-14696800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr5:14691000-14697200	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr5:14691000-14697600	Strong transcription	Adipose Nuclei	Adipose

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