Variant report

Variant	rs6414377
Chromosome Location	chr3:150840227-150840228
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:150839387..150842321-chr3:150844225..150846758,2	K562	blood:

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1003246	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1005726	0.94[CEU][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs10755104	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10935825	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10935826	0.83[EUR][1000 genomes]
rs10935827	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10935828	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11914598	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11919212	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs12489984	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13434276	0.87[ASN][1000 genomes]
rs1346943	0.95[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1431492	0.91[EUR][1000 genomes]
rs1431493	0.92[EUR][1000 genomes]
rs16863172	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1835668	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1897296	1.00[ASW][hapmap];0.89[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1920392	1.00[CEU][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2014240	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2060081	0.94[CEU][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28690162	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3773615	0.94[CEU][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs3915228	1.00[CEU][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61184267	0.92[EUR][1000 genomes]
rs6440721	0.81[EUR][1000 genomes]
rs6765294	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs6765711	0.82[JPT][hapmap]
rs6767918	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6772640	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6780120	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6787683	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6790661	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6800064	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6801591	0.92[EUR][1000 genomes]
rs6809388	0.89[CEU][hapmap]
rs6809705	0.89[CEU][hapmap];0.84[TSI][hapmap]
rs7427471	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs747205	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7633492	0.90[EUR][1000 genomes]
rs7645665	1.00[CEU][hapmap];0.83[GIH][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs9289832	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs9683109	0.88[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs970235	0.95[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9813224	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9822304	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9823077	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs9829728	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs9848163	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9850016	0.88[ASN][1000 genomes]
rs9876500	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs9883677	0.81[JPT][hapmap]

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	nsv915879	chr3:150607390-150860207	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv829756	chr3:150692636-150889738	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv460894	chr3:150770614-151095093	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv592045	chr3:150770614-151095093	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv2757897	chr3:150791625-150957485	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv2759188	chr3:150791625-150957485	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv877648	chr3:150792444-150895145	Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6414377	CLRN1	cis	parietal	SCAN
rs6414377	DHX36	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150819800-150847600	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr3:150823200-150843000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr3:150826000-150855200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:150826400-150863600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:150826600-150846400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:150826600-150851800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr3:150826600-150855000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr3:150826800-150841600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:150826800-150846600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:150827200-150847400	Weak transcription	Placenta	Placenta
11	chr3:150827400-150873000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:150827600-150855000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:150827800-150846400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr3:150827800-150847400	Weak transcription	Fetal Intestine Large	intestine
15	chr3:150828800-150845600	Weak transcription	Fetal Muscle Leg	muscle
16	chr3:150830400-150863000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:150830800-150842800	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr3:150831000-150840400	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr3:150831200-150842800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr3:150831200-150863000	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr3:150831400-150842600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:150833600-150852000	Weak transcription	Dnd41	blood
23	chr3:150834400-150844400	Weak transcription	Brain Angular Gyrus	brain
24	chr3:150837400-150845800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:150839600-150846000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr3:150839800-150840800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:150839800-150844000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:150840200-150840800	Enhancers	Fetal Lung	lung
29	chr3:150840200-150841800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:150840200-150844000	Strong transcription	Primary neutrophils fromperipheralblood	blood

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