Variant report

Variant	rs2004806
Chromosome Location	chr12:105157690-105157691
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1038968	0.85[EUR][1000 genomes]
rs1389610	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1389611	0.85[EUR][1000 genomes]
rs2047124	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2088019	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2131806	0.81[EUR][1000 genomes]
rs2245929	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2453154	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2453155	0.86[EUR][1000 genomes]
rs2463020	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2463431	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2463434	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2463435	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2468082	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2468110	0.83[EUR][1000 genomes]
rs2468112	0.90[EUR][1000 genomes]
rs2642109	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2730295	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2731030	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6539167	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs903247	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv899496	chr12:105152391-105199038	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv899497	chr12:105155291-105247010	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv560052	chr12:105155815-105157975	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2004806	CHST11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105142400-105160800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:105142600-105158000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr12:105142800-105158200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr12:105143800-105160800	Weak transcription	Fetal Muscle Leg	muscle
5	chr12:105144000-105158200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr12:105144200-105158000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr12:105145200-105158200	Weak transcription	Adipose Nuclei	Adipose
8	chr12:105145400-105161200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr12:105145600-105162800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:105145800-105161200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr12:105145800-105161200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr12:105145800-105161400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr12:105146000-105161400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr12:105146800-105161200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr12:105151400-105158400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr12:105151400-105161200	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr12:105151600-105158400	Weak transcription	Ovary	ovary
18	chr12:105151600-105160800	Weak transcription	Esophagus	oesophagus
19	chr12:105151600-105161800	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr12:105151600-105162800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:105152200-105158000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr12:105152400-105162600	Weak transcription	Brain Anterior Caudate	brain
23	chr12:105152600-105158000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr12:105152600-105158400	Weak transcription	Placenta	Placenta
25	chr12:105153000-105158000	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr12:105153000-105158000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr12:105153200-105161800	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr12:105153600-105158000	Weak transcription	Fetal Thymus	thymus
29	chr12:105153800-105158000	Weak transcription	Thymus	Thymus
30	chr12:105154000-105158200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr12:105154200-105158000	Weak transcription	Primary B cells from peripheral blood	blood
32	chr12:105154400-105158200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr12:105154400-105162800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr12:105155000-105158000	Weak transcription	Primary T cells from cord blood	blood
35	chr12:105156200-105159000	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr12:105156200-105160800	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr12:105156200-105160800	Weak transcription	Brain Germinal Matrix	brain
38	chr12:105156200-105163000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr12:105156400-105158000	Enhancers	Primary hematopoietic stem cells	blood
40	chr12:105156400-105159000	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr12:105156400-105161400	Weak transcription	Fetal Brain Male	brain
42	chr12:105156600-105158200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr12:105156800-105158400	Enhancers	GM12878-XiMat	blood
44	chr12:105156800-105159000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr12:105156800-105159200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
46	chr12:105156800-105159200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr12:105156800-105159200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr12:105157000-105159000	Enhancers	K562	blood
49	chr12:105157000-105159800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr12:105157200-105159200	Enhancers	Primary T helper cells PMA-I stimulated	--

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