Variant report

Variant	rs2639998
Chromosome Location	chr3:141336708-141336709
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:141331251..141333372-chr3:141334736..141336860,2	K562	blood:
2	chr3:141331872..141333537-chr3:141335143..141336860,2	K562	blood:
3	chr3:141323458..141325878-chr3:141335451..141337403,2	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11711375	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11916906	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11917587	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs13062809	0.86[EUR][1000 genomes]
rs13069717	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1366042	0.88[CEU][hapmap];0.95[YRI][hapmap]
rs1493209	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1582875	0.89[CEU][hapmap];0.95[YRI][hapmap]
rs16851435	0.89[JPT][hapmap]
rs16851438	0.94[JPT][hapmap]
rs16851441	0.89[JPT][hapmap]
rs16851483	0.88[JPT][hapmap]
rs1863867	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs2035935	0.88[JPT][hapmap]
rs2035936	0.82[JPT][hapmap]
rs2042864	0.89[CEU][hapmap];0.95[YRI][hapmap]
rs2172471	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2312193	0.84[CEU][hapmap];0.88[JPT][hapmap]
rs2639997	0.88[JPT][hapmap]
rs2640017	0.88[JPT][hapmap]
rs295299	0.88[JPT][hapmap]
rs295300	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs295320	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs295323	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35711802	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3732869	0.89[JPT][hapmap]
rs3806646	0.93[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs3821709	0.88[JPT][hapmap]
rs3821710	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3821712	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4683610	0.88[JPT][hapmap]
rs6440013	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6440015	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6763498	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6767158	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6776003	0.87[ASN][1000 genomes]
rs6785874	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6795168	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6800122	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6808837	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7627807	0.88[JPT][hapmap]
rs7632308	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs7643837	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.80[AFR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9813177	0.92[CEU][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9878347	0.94[JPT][hapmap];0.87[YRI][hapmap]
rs9879503	0.94[JPT][hapmap];0.87[YRI][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	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2639998	RASA2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141277200-141341400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:141313200-141344000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:141320400-141337200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr3:141321800-141342600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:141325000-141338000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:141330000-141338800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:141330200-141338200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr3:141330400-141337000	Weak transcription	Lung	lung
9	chr3:141330400-141337400	Weak transcription	HSMMtube	muscle
10	chr3:141330400-141337800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr3:141330400-141338000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr3:141330400-141342000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr3:141330400-141342000	Weak transcription	Pancreas	Pancrea
14	chr3:141330400-141343200	Weak transcription	Brain Angular Gyrus	brain
15	chr3:141330400-141344000	Weak transcription	HMEC	breast
16	chr3:141330400-141344600	Weak transcription	NHLF	lung
17	chr3:141330600-141336800	Weak transcription	Thymus	Thymus
18	chr3:141330600-141337600	Weak transcription	Brain Germinal Matrix	brain
19	chr3:141330600-141338000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr3:141330600-141338200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:141330600-141339000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr3:141330600-141339200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr3:141330600-141344200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:141330600-141344200	Weak transcription	Ovary	ovary
25	chr3:141330800-141338400	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr3:141330800-141338400	Weak transcription	Left Ventricle	heart
27	chr3:141330800-141344200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:141331600-141338800	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr3:141331800-141338600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr3:141332000-141337600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr3:141332000-141344600	Weak transcription	NHDF-Ad	bronchial
32	chr3:141332200-141336800	Weak transcription	Liver	Liver
33	chr3:141332200-141337000	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr3:141332200-141337600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr3:141332200-141338200	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr3:141332200-141339200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr3:141332400-141337000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr3:141332400-141337000	Weak transcription	Duodenum Mucosa	Duodenum
39	chr3:141332400-141339200	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr3:141332400-141340600	Weak transcription	A549	lung
41	chr3:141332400-141344200	Weak transcription	HSMM	muscle
42	chr3:141332400-141344400	Weak transcription	Osteobl	bone
43	chr3:141332400-141345800	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr3:141332600-141337000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr3:141333000-141337000	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr3:141333400-141337000	Weak transcription	Primary hematopoietic stem cells	blood
47	chr3:141333600-141337400	Weak transcription	Rectal Smooth Muscle	rectum
48	chr3:141333600-141344200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr3:141334000-141338000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr3:141334000-141339000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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