Variant report

Variant	rs10519963
Chromosome Location	chr4:149297675-149297676
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10434100	1.00[CEU][hapmap];0.80[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10434128	0.93[CEU][hapmap];0.80[CHB][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs10434129	0.87[EUR][1000 genomes]
rs11099692	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11722067	0.91[JPT][hapmap]
rs11931777	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12506058	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12510074	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1398269	0.91[JPT][hapmap]
rs1512328	0.91[JPT][hapmap]
rs1512335	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs16998733	0.93[CEU][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs17024681	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs17484783	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs17484839	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs17484873	1.00[ASW][hapmap];0.93[CEU][hapmap];0.96[LWK][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs17485033	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs17582031	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs1877445	0.82[JPT][hapmap]
rs1913023	0.91[JPT][hapmap]
rs2048546	0.93[CEU][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs2048547	0.82[JPT][hapmap]
rs2063553	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2063554	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2063555	1.00[CEU][hapmap];0.80[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2063556	0.81[CEU][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2137330	1.00[CEU][hapmap];0.80[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34296798	0.89[EUR][1000 genomes]
rs4835513	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56721167	0.88[EUR][1000 genomes]
rs59941204	0.96[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs61569758	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61756947	0.96[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs61758341	0.86[EUR][1000 genomes]
rs61758351	0.86[EUR][1000 genomes]
rs61763850	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61764769	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66584597	0.86[EUR][1000 genomes]
rs6825048	0.91[JPT][hapmap]
rs6829009	0.87[EUR][1000 genomes]
rs6834935	0.93[CEU][hapmap];0.82[GIH][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs6840422	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs72728499	0.82[EUR][1000 genomes]
rs72729936	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72729950	0.81[EUR][1000 genomes]
rs72729990	0.88[EUR][1000 genomes]
rs72729992	0.96[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs72732304	0.86[EUR][1000 genomes]
rs72732308	0.86[EUR][1000 genomes]
rs72732311	0.86[EUR][1000 genomes]
rs72953910	0.96[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7682972	0.89[EUR][1000 genomes]
rs7686433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7698307	0.93[CEU][hapmap];0.82[GIH][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027263	chr4:149127120-149320135	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv537296	chr4:149127120-149320135	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1016966	chr4:149209467-149341037	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv530433	chr4:149277637-149669181	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv880246	chr4:149287807-149311728	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10519963	FCRL1	trans	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:149277000-149306800	Weak transcription	Pancreas	Pancrea
2	chr4:149281200-149300800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr4:149283000-149299000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr4:149292200-149298600	Weak transcription	Left Ventricle	heart
5	chr4:149292200-149315000	Weak transcription	Fetal Muscle Leg	muscle
6	chr4:149296200-149298000	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr4:149296600-149297800	Enhancers	Dnd41	blood
8	chr4:149296800-149297800	Enhancers	Primary hematopoietic stem cells	blood
9	chr4:149296800-149297800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr4:149296800-149297800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr4:149296800-149297800	Active TSS	Right Atrium	heart
12	chr4:149296800-149297800	Enhancers	Stomach Mucosa	stomach
13	chr4:149296800-149297800	Active TSS	Stomach Smooth Muscle	stomach
14	chr4:149296800-149297800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr4:149296800-149298000	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr4:149296800-149298000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr4:149296800-149298600	Enhancers	HepG2	liver
18	chr4:149296800-149299600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr4:149297000-149297800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
20	chr4:149297000-149297800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
21	chr4:149297000-149297800	Active TSS	Brain Anterior Caudate	brain
22	chr4:149297000-149297800	Enhancers	Duodenum Mucosa	Duodenum
23	chr4:149297000-149297800	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr4:149297000-149297800	Active TSS	Skeletal Muscle Male	skeletal muscle
25	chr4:149297000-149297800	Flanking Active TSS	HUVEC	blood vessel
26	chr4:149297000-149299200	Enhancers	Fetal Heart	heart
27	chr4:149297200-149297800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr4:149297200-149297800	Active TSS	Aorta	Aorta
29	chr4:149297200-149297800	Active TSS	Brain Angular Gyrus	brain
30	chr4:149297200-149297800	Active TSS	Brain Substantia Nigra	brain
31	chr4:149297200-149297800	Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr4:149297200-149297800	Enhancers	NHEK	skin
33	chr4:149297400-149297800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
34	chr4:149297400-149297800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
35	chr4:149297400-149297800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr4:149297400-149297800	Flanking Active TSS	Brain Cingulate Gyrus	brain
37	chr4:149297400-149297800	Enhancers	NHLF	lung
38	chr4:149297600-149297800	Enhancers	Primary T cells fromperipheralblood	blood
39	chr4:149297600-149297800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr4:149297600-149297800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
41	chr4:149297600-149297800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr4:149297600-149297800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr4:149297600-149297800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr4:149297600-149297800	Enhancers	Liver	Liver
45	chr4:149297600-149297800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
46	chr4:149297600-149297800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
47	chr4:149297600-149297800	Enhancers	Rectal Smooth Muscle	rectum
48	chr4:149297600-149298400	Weak transcription	Psoas Muscle	Psoas
49	chr4:149297600-149298600	Weak transcription	Ovary	ovary
50	chr4:149297600-149298800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

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