Variant report

Variant	rs743660
Chromosome Location	chr3:46402018-46402019
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	chr3:46395645..46397767-chr3:46399914..46402472,2	K562	blood:

Extended variants
information (count: 10 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1799865	0.90[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap]
rs3092962	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs3092963	0.90[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap]
rs3762823	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs3918358	0.90[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap]
rs6441971	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7371987	0.81[MEX][hapmap];0.84[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv3323840	chr3:46352348-46497196	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv3389382	chr3:46352798-46496696	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs743660	SLC26A6	cis	cerebellum	SCAN
rs743660	HIGD1A	cis	parietal	SCAN
rs743660	CXCR6	cis	parietal	SCAN
rs743660	SLC25A20	cis	cerebellum	SCAN
rs743660	DALRD3	cis	cerebellum	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46392400-46402600	Weak transcription	Spleen	Spleen
2	chr3:46395800-46404200	Weak transcription	Right Atrium	heart
3	chr3:46396000-46422000	Weak transcription	Lung	lung
4	chr3:46398000-46404200	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr3:46398600-46402800	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
6	chr3:46399400-46404000	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr3:46400200-46404200	Enhancers	Primary T cells fromperipheralblood	blood
8	chr3:46400400-46404200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr3:46400400-46404400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr3:46400600-46403000	Enhancers	Fetal Stomach	stomach
11	chr3:46400600-46404000	Enhancers	Primary B cells from cord blood	blood
12	chr3:46400800-46402200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
13	chr3:46400800-46403200	Enhancers	Brain Germinal Matrix	brain
14	chr3:46400800-46403400	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr3:46400800-46403800	Enhancers	Primary hematopoietic stem cells	blood
16	chr3:46401000-46402200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr3:46401000-46402400	Flanking Active TSS	GM12878-XiMat	blood
18	chr3:46401000-46402600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:46401000-46403000	Enhancers	Brain Anterior Caudate	brain
20	chr3:46401000-46403000	Enhancers	Brain Hippocampus Middle	brain
21	chr3:46401000-46403000	Enhancers	HSMMtube	muscle
22	chr3:46401000-46403200	Enhancers	Adipose Nuclei	Adipose
23	chr3:46401000-46403200	Enhancers	HSMM	muscle
24	chr3:46401000-46403400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr3:46401000-46403800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
26	chr3:46401000-46404000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:46401000-46404000	Enhancers	Fetal Thymus	thymus
28	chr3:46401000-46404200	Enhancers	Primary B cells from peripheral blood	blood
29	chr3:46401000-46404400	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr3:46401000-46404600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr3:46401200-46402200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr3:46401200-46402200	Enhancers	Fetal Lung	lung
33	chr3:46401200-46402800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr3:46401200-46402800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr3:46401200-46403200	Enhancers	NHDF-Ad	bronchial
36	chr3:46401200-46403600	Enhancers	Brain Substantia Nigra	brain
37	chr3:46401400-46402200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr3:46401400-46402200	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr3:46401400-46402200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
40	chr3:46401400-46402800	Enhancers	Fetal Brain Male	brain
41	chr3:46401400-46403000	Genic enhancers	Primary monocytes fromperipheralblood	blood
42	chr3:46401400-46403000	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr3:46401600-46402600	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr3:46401600-46403400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:46401600-46403800	Enhancers	Duodenum Mucosa	Duodenum
46	chr3:46401800-46402200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr3:46401800-46403200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:46401800-46403400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr3:46402000-46402400	Weak transcription	Fetal Muscle Leg	muscle
50	chr3:46402000-46402600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--

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