Variant report

Variant	rs10434100
Chromosome Location	chr4:149287807-149287808
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10434128	0.93[CEU][hapmap];0.80[CHB][hapmap];0.81[GIH][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10434129	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10434130	0.94[ASN][1000 genomes]
rs10519963	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]
rs11099692	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11722067	0.91[JPT][hapmap]
rs11931777	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12506058	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12510074	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1398269	0.91[JPT][hapmap]
rs1512328	0.91[JPT][hapmap]
rs1512335	0.82[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs16998733	0.93[CEU][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs17024681	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs17484783	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17484839	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs17484873	0.93[CEU][hapmap];0.87[GIH][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs17485033	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs17582031	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs1877445	0.82[JPT][hapmap]
rs1913023	0.91[JPT][hapmap]
rs2048546	0.93[CEU][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs2048547	0.82[JPT][hapmap]
rs2063553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2063554	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2063555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2063556	0.81[CEU][hapmap];0.90[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2137330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34296798	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4835513	0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56721167	0.84[EUR][1000 genomes]
rs59941204	0.84[EUR][1000 genomes]
rs61569758	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61756947	0.84[EUR][1000 genomes]
rs61758341	0.83[EUR][1000 genomes]
rs61758351	0.83[EUR][1000 genomes]
rs61763850	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61764769	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs66584597	0.83[EUR][1000 genomes]
rs6825048	0.91[JPT][hapmap]
rs6829009	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6834935	0.93[CEU][hapmap];0.93[GIH][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs6840422	0.93[CEU][hapmap];0.92[GIH][hapmap];0.83[EUR][1000 genomes]
rs72728499	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72729936	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72729950	0.84[EUR][1000 genomes]
rs72729990	0.84[EUR][1000 genomes]
rs72729992	0.84[EUR][1000 genomes]
rs72732304	0.83[EUR][1000 genomes]
rs72732308	0.83[EUR][1000 genomes]
rs72732311	0.83[EUR][1000 genomes]
rs72953910	0.84[EUR][1000 genomes]
rs7682972	0.85[EUR][1000 genomes]
rs7686433	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7698307	0.93[CEU][hapmap];0.93[GIH][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	esv3584816	chr4:149254670-149293317	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	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
6	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10434100	FCRL1	trans	cerebellum	SCAN
rs10434100	LSM6	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:149268200-149288000	Weak transcription	Small Intestine	intestine
2	chr4:149277000-149291000	Weak transcription	Left Ventricle	heart
3	chr4:149277000-149296800	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr4:149277000-149306800	Weak transcription	Pancreas	Pancrea
5	chr4:149281200-149300800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr4:149281400-149290800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr4:149282200-149289000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr4:149282200-149289000	Weak transcription	Gastric	stomach
9	chr4:149282800-149289200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr4:149282800-149296800	Weak transcription	Psoas Muscle	Psoas
11	chr4:149283000-149289000	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr4:149283000-149299000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr4:149283200-149293400	Weak transcription	Right Atrium	heart
14	chr4:149284200-149288000	Weak transcription	Colon Smooth Muscle	Colon
15	chr4:149287800-149288000	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr4:149287800-149288200	Enhancers	Duodenum Smooth Muscle	Duodenum
17	chr4:149287800-149288400	Enhancers	Fetal Heart	heart
18	chr4:149287800-149288400	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr4:149287800-149289600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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