Variant report

Variant	rs1543876
Chromosome Location	chr1:179279809-179279810
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:179279593..179281355-chr1:179292401..179294402,2	K562	blood:
2	chr1:179279773..179281355-chr1:179292902..179294753,2	K562	blood:

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs12749666	0.88[GIH][hapmap]
rs2152318	0.88[GIH][hapmap]
rs2250477	0.88[GIH][hapmap]
rs2255375	0.86[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs2274229	1.00[JPT][hapmap]
rs2492778	0.88[GIH][hapmap]
rs2493117	0.88[GIH][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005278	chr1:179197645-179371395	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1543876	TDRD5	cis	parietal	SCAN
rs1543876	RASAL2	cis	parietal	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179263800-179304600	Weak transcription	Lung	lung
2	chr1:179263800-179306400	Weak transcription	Gastric	stomach
3	chr1:179264200-179290200	Weak transcription	Aorta	Aorta
4	chr1:179264600-179281200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:179264600-179292000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr1:179264600-179304600	Weak transcription	Right Ventricle	heart
7	chr1:179264600-179310200	Weak transcription	Brain Substantia Nigra	brain
8	chr1:179264600-179314000	Weak transcription	Brain Angular Gyrus	brain
9	chr1:179264600-179314000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr1:179264800-179313800	Weak transcription	Brain Hippocampus Middle	brain
11	chr1:179264800-179313800	Weak transcription	Fetal Brain Female	brain
12	chr1:179264800-179334200	Weak transcription	Colon Smooth Muscle	Colon
13	chr1:179265400-179287600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:179266400-179286400	Weak transcription	Fetal Kidney	kidney
15	chr1:179266400-179322800	Weak transcription	Small Intestine	intestine
16	chr1:179267800-179287000	Weak transcription	Spleen	Spleen
17	chr1:179268400-179280200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:179268400-179312000	Weak transcription	Fetal Thymus	thymus
19	chr1:179269600-179280000	Weak transcription	Thymus	Thymus
20	chr1:179270200-179283200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:179271400-179287600	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr1:179271600-179283800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr1:179271600-179286400	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr1:179271800-179280200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:179271800-179287600	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr1:179272000-179284400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr1:179272000-179286000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:179272600-179288200	Weak transcription	Stomach Mucosa	stomach
29	chr1:179272600-179313800	Weak transcription	Brain Anterior Caudate	brain
30	chr1:179273000-179281400	Weak transcription	Adipose Nuclei	Adipose
31	chr1:179273000-179311600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr1:179273200-179290400	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr1:179273200-179294600	Weak transcription	Placenta	Placenta
34	chr1:179273400-179287000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr1:179273800-179293400	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr1:179274400-179281200	Weak transcription	Primary hematopoietic stem cells	blood
37	chr1:179274400-179289400	Weak transcription	Fetal Lung	lung
38	chr1:179274600-179281600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr1:179274600-179284200	Weak transcription	Fetal Intestine Small	intestine
40	chr1:179274600-179302400	Weak transcription	Left Ventricle	heart
41	chr1:179274600-179304400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr1:179274600-179306000	Weak transcription	Stomach Smooth Muscle	stomach
43	chr1:179274800-179281400	Weak transcription	GM12878-XiMat	blood
44	chr1:179275200-179281600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr1:179275600-179311600	Weak transcription	HUVEC	blood vessel
46	chr1:179276400-179306200	Weak transcription	Fetal Muscle Trunk	muscle
47	chr1:179276600-179281600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr1:179276600-179281600	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr1:179276600-179282000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr1:179276600-179283200	Weak transcription	Cortex derived primary cultured neurospheres	brain

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