Variant report

Variant	rs12516085
Chromosome Location	chr5:94822053-94822054
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:94815715..94817542-chr5:94820797..94823312,2	K562	blood:
2	chr5:94821124..94823692-chr5:94830042..94832328,2	K562	blood:

Variant related genes	Relation type
ENSG00000198677	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs12657120	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2731829	0.86[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.95[ASN][1000 genomes]
rs4639250	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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	nsv882388	chr5:94764006-94925849	Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv598954	chr5:94783175-94859599	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12516085	LIX1	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:94795200-94826600	Weak transcription	NHEK	skin
2	chr5:94799200-94834800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:94804600-94823000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr5:94808200-94822800	Weak transcription	Psoas Muscle	Psoas
5	chr5:94809000-94823400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr5:94809800-94823000	Strong transcription	Primary B cells from peripheral blood	blood
7	chr5:94810200-94823000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr5:94810200-94823000	Strong transcription	Dnd41	blood
9	chr5:94810200-94823000	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr5:94810200-94823200	Strong transcription	Primary T helper cells PMA-I stimulated	--
11	chr5:94810200-94827400	Strong transcription	Fetal Thymus	thymus
12	chr5:94810600-94823000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr5:94810600-94823000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr5:94810600-94823200	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr5:94810600-94827600	Strong transcription	Placenta	Placenta
16	chr5:94810800-94823200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr5:94810800-94823200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr5:94811000-94822200	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr5:94811000-94889400	Weak transcription	Stomach Mucosa	stomach
20	chr5:94811200-94823000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr5:94811200-94835600	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr5:94811800-94822400	Weak transcription	Colonic Mucosa	Colon
23	chr5:94812400-94835600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr5:94813400-94824000	Strong transcription	Liver	Liver
25	chr5:94814000-94824200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr5:94815400-94824000	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr5:94815400-94827600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr5:94815400-94853200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr5:94815600-94823000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr5:94815600-94823200	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr5:94815800-94823200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr5:94815800-94823200	Strong transcription	Primary T cells from cord blood	blood
33	chr5:94816000-94823000	Strong transcription	Left Ventricle	heart
34	chr5:94816000-94824000	Strong transcription	Muscle Satellite Cultured Cells	--
35	chr5:94816200-94822800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr5:94816200-94822800	Strong transcription	Fetal Brain Female	brain
37	chr5:94816200-94823000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr5:94816200-94823000	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr5:94816200-94823000	Strong transcription	Fetal Muscle Leg	muscle
40	chr5:94816200-94824200	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr5:94816200-94827400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr5:94816200-94827400	Strong transcription	HUVEC	blood vessel
43	chr5:94816400-94827400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr5:94816400-94827400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
45	chr5:94816600-94823200	Strong transcription	Duodenum Mucosa	Duodenum
46	chr5:94816800-94824000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr5:94816800-94827400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr5:94817200-94822400	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr5:94817200-94849000	Weak transcription	Small Intestine	intestine
50	chr5:94817400-94822200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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