Variant report

Variant	rs3821710
Chromosome Location	chr3:141301451-141301452
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:141301255..141303348-chr3:141304484..141306146,2	K562	blood:
2	chr3:141299643..141301843-chr3:141308468..141311186,2	MCF-7	breast:
3	chr3:141300234..141304209-chr3:141304484..141307292,3	K562	blood:

Variant related genes	Relation type
ENSG00000155903	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11711375	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11916906	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11917587	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13062809	0.89[EUR][1000 genomes]
rs13069717	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1366042	0.96[CEU][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs1493209	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1582875	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs16851435	0.87[CHD][hapmap];0.88[JPT][hapmap]
rs16851438	0.94[JPT][hapmap]
rs16851441	0.88[JPT][hapmap]
rs16851483	0.88[JPT][hapmap]
rs1863867	0.81[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2035935	0.88[JPT][hapmap]
rs2035936	0.81[JPT][hapmap]
rs2042864	0.96[CEU][hapmap]
rs2172471	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2312193	0.92[CEU][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap]
rs2639997	0.88[JPT][hapmap]
rs2639998	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2640017	0.88[JPT][hapmap]
rs295299	0.88[JPT][hapmap]
rs295300	0.92[CHD][hapmap];0.88[JPT][hapmap]
rs295320	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs295323	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35711802	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3732869	0.88[JPT][hapmap]
rs3806646	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3821709	0.87[JPT][hapmap]
rs3821712	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4683610	0.88[JPT][hapmap]
rs6440013	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440015	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6763498	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6767158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6776003	0.89[CEU][hapmap];0.91[ASN][1000 genomes]
rs6785874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6795168	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6800122	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6808837	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7612543	0.82[TSI][hapmap]
rs7627807	0.88[JPT][hapmap]
rs7632308	1.00[CEU][hapmap];0.84[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs7643837	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9813177	1.00[CEU][hapmap];0.84[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9850416	0.82[TSI][hapmap]
rs9851256	0.87[CEU][hapmap]
rs9878347	0.94[JPT][hapmap]
rs9879503	0.94[JPT][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	esv1795799	chr3:141284383-141301451	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv1794809	chr3:141290177-141304631	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3821710	GK5	cis	parietal	SCAN
rs3821710	ZBTB38	cis	cerebellum	SCAN
rs3821710	RASA2	cis	cerebellum	SCAN
rs3821710	RASA2	cis	parietal	SCAN
rs3821710	RASA2	Cis_1M	lymphoblastoid	RTeQTL
rs3821710	ATP1B3	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141236400-141306600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr3:141254800-141319200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:141255200-141304800	Weak transcription	Ovary	ovary
4	chr3:141255200-141320000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:141255400-141319200	Weak transcription	Aorta	Aorta
6	chr3:141265200-141336200	Weak transcription	Psoas Muscle	Psoas
7	chr3:141272600-141319200	Strong transcription	Dnd41	blood
8	chr3:141275800-141320600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:141276400-141329400	Weak transcription	Small Intestine	intestine
10	chr3:141277200-141341400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr3:141277800-141312000	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr3:141281800-141329400	Weak transcription	Fetal Brain Male	brain
13	chr3:141288000-141312400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:141288200-141320000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr3:141288400-141316400	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr3:141288600-141302800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr3:141288600-141308400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:141288600-141316400	Strong transcription	Primary B cells from peripheral blood	blood
19	chr3:141289000-141311800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:141289000-141316600	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr3:141289200-141309000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr3:141289200-141316400	Strong transcription	Fetal Thymus	thymus
23	chr3:141289400-141301600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:141290200-141301600	Strong transcription	NH-A	brain
25	chr3:141293800-141319000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr3:141294800-141319200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr3:141295000-141319200	Weak transcription	Esophagus	oesophagus
28	chr3:141295200-141320000	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr3:141295400-141314000	Weak transcription	Colonic Mucosa	Colon
30	chr3:141295600-141319600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr3:141295600-141320000	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr3:141295800-141301800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr3:141295800-141303600	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr3:141295800-141313000	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr3:141295800-141316400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:141295800-141320800	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr3:141296000-141316000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr3:141296200-141309000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr3:141296400-141303800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr3:141296400-141307000	Strong transcription	Liver	Liver
41	chr3:141296400-141307600	Strong transcription	HSMM	muscle
42	chr3:141296600-141307400	Strong transcription	Duodenum Mucosa	Duodenum
43	chr3:141296600-141312200	Strong transcription	Primary B cells from cord blood	blood
44	chr3:141296800-141302000	Strong transcription	Primary T killer memory cells from peripheral blood	blood
45	chr3:141296800-141307600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
46	chr3:141296800-141307800	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr3:141296800-141310800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr3:141296800-141316400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr3:141296800-141316600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr3:141297000-141302800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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