Variant report

Variant	rs4835310
Chromosome Location	chr4:147379015-147379016
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10001383	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10011222	0.83[EUR][1000 genomes]
rs10012310	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10017463	0.86[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10018860	0.87[CEU][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10024266	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs10026558	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs10030464	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10032453	0.90[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11100926	0.90[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11726588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11726594	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11727219	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11734649	0.87[CEU][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11940327	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13105153	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13110748	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13134417	0.88[EUR][1000 genomes]
rs13134849	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13149918	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13151354	0.88[EUR][1000 genomes]
rs13435029	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17769016	0.87[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2244306	0.86[MEX][hapmap]
rs2356822	0.86[MEX][hapmap]
rs2630279	0.94[GIH][hapmap];0.86[MEX][hapmap]
rs2679138	0.88[GIH][hapmap]
rs3849037	0.87[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3914627	0.81[EUR][1000 genomes]
rs3914629	0.88[EUR][1000 genomes]
rs4407528	0.86[MEX][hapmap]
rs4835037	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4835040	0.87[CEU][hapmap];0.80[TSI][hapmap];0.88[EUR][1000 genomes]
rs4835307	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4835312	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4835313	0.86[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4835314	0.87[CEU][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4835315	0.86[CEU][hapmap];0.88[EUR][1000 genomes]
rs4835316	0.86[CEU][hapmap];0.80[TSI][hapmap];0.88[EUR][1000 genomes]
rs6537419	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6537421	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6537423	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6537424	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6537425	0.88[EUR][1000 genomes]
rs6537426	0.85[EUR][1000 genomes]
rs6812728	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6815417	0.88[EUR][1000 genomes]
rs6816737	0.87[CEU][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes]
rs6819042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6829209	0.87[CEU][hapmap];0.80[TSI][hapmap];0.88[EUR][1000 genomes]
rs6837453	0.87[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6846498	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6849958	0.81[CEU][hapmap];0.88[EUR][1000 genomes]
rs7435019	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7437083	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs7439061	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs7439429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7670877	0.94[GIH][hapmap];0.86[MEX][hapmap]
rs7687182	0.88[EUR][1000 genomes]
rs7687917	0.88[EUR][1000 genomes]
rs9992118	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9995307	0.82[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9995820	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461675	chr4:147116864-147768206	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv595651	chr4:147116864-147768206	Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1033640	chr4:147232217-147531881	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv917053	chr4:147265436-147499653	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1023868	chr4:147265443-147531626	Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
6	nsv537293	chr4:147265443-147531626	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
7	nsv428453	chr4:147335953-147457115	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4835310	TTC29	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:147364600-147388000	Weak transcription	NHEK	skin
2	chr4:147364800-147402200	Weak transcription	Thymus	Thymus
3	chr4:147366600-147379200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr4:147367200-147385000	Weak transcription	Left Ventricle	heart
5	chr4:147370800-147388800	Weak transcription	Psoas Muscle	Psoas
6	chr4:147371800-147379200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr4:147372000-147402400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr4:147372200-147389000	Weak transcription	Primary B cells from cord blood	blood
9	chr4:147372800-147379200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr4:147373200-147379200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr4:147373200-147394000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr4:147375200-147379800	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr4:147375200-147386400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:147377600-147380200	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr4:147378000-147382200	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr4:147378200-147379600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr4:147378200-147379600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr4:147378200-147379800	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr4:147378200-147382400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr4:147378600-147379400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr4:147378600-147380000	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr4:147378800-147379600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr4:147378800-147380200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr4:147378800-147380800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr4:147379000-147379800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr4:147379000-147380000	Enhancers	Primary T cells from cord blood	blood

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