Variant report

Variant	rs2596668
Chromosome Location	chr3:17219137-17219138
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs13318886	0.85[CEU][hapmap]
rs1374197	0.85[CEU][hapmap]
rs1449882	0.85[CEU][hapmap]
rs1463222	0.82[CEU][hapmap]
rs17043492	0.85[CEU][hapmap]
rs1867772	0.92[CEU][hapmap]
rs187303	0.82[CEU][hapmap]
rs2060623	0.85[CEU][hapmap]
rs2060627	0.82[CEU][hapmap]
rs2247106	0.81[CEU][hapmap]
rs2348004	0.81[CEU][hapmap]
rs2348005	0.85[CEU][hapmap]
rs2470347	0.82[CEU][hapmap]
rs2470583	0.84[CEU][hapmap]
rs2592099	0.82[CEU][hapmap]
rs2596637	0.82[CEU][hapmap]
rs2596643	0.82[CEU][hapmap]
rs2596645	0.80[CEU][hapmap]
rs2596648	0.85[CEU][hapmap]
rs2596650	0.85[CEU][hapmap]
rs2596662	0.85[CEU][hapmap]
rs2596674	0.81[CEU][hapmap]
rs2596675	0.81[CEU][hapmap]
rs2596679	0.82[CEU][hapmap]
rs2733479	0.82[CEU][hapmap]
rs2733485	0.81[CEU][hapmap]
rs2733487	0.82[CEU][hapmap]
rs2733491	0.82[CEU][hapmap]
rs2733492	0.85[CEU][hapmap]
rs2733495	0.85[CEU][hapmap]
rs2733496	0.85[CEU][hapmap]
rs2733498	0.82[CEU][hapmap]
rs2733501	0.82[CEU][hapmap]
rs2733502	0.84[CEU][hapmap]
rs2733514	0.82[CEU][hapmap]
rs2733515	0.82[CEU][hapmap]
rs2733519	0.81[CEU][hapmap]
rs2733523	0.81[CEU][hapmap]
rs283906	0.82[CEU][hapmap]
rs283907	0.82[CEU][hapmap]
rs283909	0.82[CEU][hapmap]
rs283912	0.82[CEU][hapmap]
rs283915	0.82[CEU][hapmap]
rs283916	0.82[CEU][hapmap]
rs283917	0.82[CEU][hapmap]
rs283925	0.82[CEU][hapmap]
rs283930	0.85[CEU][hapmap]
rs283936	0.85[CEU][hapmap]
rs283940	0.85[CEU][hapmap]
rs283941	0.82[CEU][hapmap]
rs283943	0.82[CEU][hapmap]
rs283945	0.85[CEU][hapmap]
rs283946	0.82[CEU][hapmap]
rs283947	0.82[CEU][hapmap]
rs283948	0.82[CEU][hapmap]
rs283949	0.82[CEU][hapmap]
rs6762516	0.85[CEU][hapmap]
rs6763593	0.85[CEU][hapmap]
rs6801690	0.81[CEU][hapmap]
rs7617933	0.82[CEU][hapmap]
rs9817290	0.89[CEU][hapmap]
rs9820703	0.85[CEU][hapmap]
rs9830240	0.85[CEU][hapmap]
rs9848766	0.85[CEU][hapmap]
rs9850127	0.85[CEU][hapmap]

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	nsv589841	chr3:17214070-17290465	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv876588	chr3:17214070-17314872	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2596668	OXNAD1	cis	cerebellum	SCAN
rs2596668	LSM3	cis	parietal	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:17195000-17224200	Weak transcription	Fetal Kidney	kidney
2	chr3:17195200-17223000	Weak transcription	Fetal Brain Female	brain
3	chr3:17198400-17225200	Weak transcription	HMEC	breast
4	chr3:17200800-17225600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:17201000-17220400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:17201200-17236200	Weak transcription	Fetal Brain Male	brain
7	chr3:17203200-17224400	Weak transcription	A549	lung
8	chr3:17203800-17244200	Weak transcription	Colonic Mucosa	Colon
9	chr3:17204400-17221200	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr3:17208000-17223600	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr3:17208200-17244000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr3:17208400-17221000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr3:17208400-17221000	Weak transcription	Brain Anterior Caudate	brain
14	chr3:17208400-17223600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:17208400-17224400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr3:17208400-17228600	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr3:17208400-17243800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr3:17208400-17244000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr3:17208600-17221000	Weak transcription	Fetal Thymus	thymus
20	chr3:17208600-17224600	Weak transcription	HepG2	liver
21	chr3:17208800-17234400	Weak transcription	Brain Angular Gyrus	brain
22	chr3:17209000-17221000	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr3:17209000-17221000	Weak transcription	GM12878-XiMat	blood
24	chr3:17209000-17234000	Weak transcription	Brain Substantia Nigra	brain
25	chr3:17209200-17220200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr3:17209200-17221000	Weak transcription	Thymus	Thymus
27	chr3:17209200-17224400	Weak transcription	Placenta	Placenta
28	chr3:17209200-17224800	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr3:17209200-17225000	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr3:17209200-17225600	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr3:17209400-17224600	Weak transcription	Fetal Lung	lung
32	chr3:17209600-17220400	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr3:17209600-17220400	Weak transcription	Dnd41	blood
34	chr3:17209600-17223000	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr3:17209600-17224400	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr3:17209600-17224400	Weak transcription	Liver	Liver
37	chr3:17209600-17224400	Weak transcription	Lung	lung
38	chr3:17209600-17224600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr3:17209600-17224600	Weak transcription	Fetal Muscle Leg	muscle
40	chr3:17209600-17234000	Weak transcription	Brain Hippocampus Middle	brain
41	chr3:17209600-17236800	Weak transcription	Gastric	stomach
42	chr3:17209800-17221000	Weak transcription	Primary T cells from cord blood	blood
43	chr3:17210000-17220800	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr3:17210000-17224400	Weak transcription	Fetal Intestine Large	intestine
45	chr3:17210000-17244000	Weak transcription	Esophagus	oesophagus
46	chr3:17210400-17224600	Weak transcription	Fetal Muscle Trunk	muscle
47	chr3:17210800-17222200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:17212200-17220200	Weak transcription	Fetal Intestine Small	intestine
49	chr3:17212200-17224600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr3:17213600-17221000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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