Variant report

Variant	rs6729359
Chromosome Location	chr2:39269446-39269447
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	chr2:39266758..39270200-chr2:39270391..39273351,3	K562	blood:
2	chr2:39267253..39269972-chr2:39274346..39276018,2	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10173380	0.90[ASN][1000 genomes]
rs10495883	0.89[ASW][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.85[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs17023241	0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs17023272	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2373466	1.00[GIH][hapmap]
rs2373497	0.89[ASW][hapmap];1.00[YRI][hapmap]
rs3112160	1.00[GIH][hapmap]
rs3112164	1.00[GIH][hapmap]
rs3112165	1.00[CHB][hapmap]
rs41280639	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs55649188	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs57362484	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs57866617	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs59340802	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs59988245	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs61049772	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs61392383	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs61521176	0.90[ASN][1000 genomes]
rs6709646	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6722478	1.00[GIH][hapmap]
rs6735371	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6755453	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs72906433	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs72906442	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs72906449	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs72906454	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs72906469	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs72918721	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7559174	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs7565814	0.82[JPT][hapmap];0.95[ASN][1000 genomes]
rs7571797	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7581411	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7583010	0.82[JPT][hapmap];1.00[ASN][1000 genomes]
rs7588123	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7592176	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7599990	0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs7605889	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7609455	0.98[AFR][1000 genomes];0.84[AMR][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	nsv873884	chr2:39154463-39332093	Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv2755359	chr2:39169049-39417849	Strong transcription Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers 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 target site	37 gene(s)	inside rSNPs	diseases
3	nsv873885	chr2:39200198-39573521	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1010874	chr2:39255376-39604535	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv535649	chr2:39255376-39604535	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv531346	chr2:39263225-39606367	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
7	nsv533348	chr2:39264345-39596169	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6729359	SOS1	cis	lymphoblastoid	seeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39213800-39308000	Weak transcription	Pancreas	Pancrea
2	chr2:39227600-39303400	Weak transcription	Colonic Mucosa	Colon
3	chr2:39229800-39293000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:39232600-39300000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:39235400-39312000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:39235600-39293200	Weak transcription	Fetal Brain Male	brain
7	chr2:39235600-39295800	Weak transcription	NHLF	lung
8	chr2:39235600-39298200	Weak transcription	Small Intestine	intestine
9	chr2:39235600-39327800	Weak transcription	Esophagus	oesophagus
10	chr2:39235800-39284000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr2:39235800-39293600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr2:39236000-39295600	Weak transcription	Aorta	Aorta
13	chr2:39236000-39295800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr2:39236000-39305600	Weak transcription	Gastric	stomach
15	chr2:39236200-39305600	Weak transcription	Lung	lung
16	chr2:39240800-39299200	Weak transcription	Brain Hippocampus Middle	brain
17	chr2:39241600-39276400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr2:39241600-39292800	Weak transcription	GM12878-XiMat	blood
19	chr2:39243200-39299600	Weak transcription	Brain Substantia Nigra	brain
20	chr2:39244600-39295400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr2:39246600-39274000	Weak transcription	Fetal Kidney	kidney
22	chr2:39250000-39282200	Weak transcription	Brain Anterior Caudate	brain
23	chr2:39250000-39292800	Weak transcription	Psoas Muscle	Psoas
24	chr2:39250200-39295200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr2:39250200-39313600	Weak transcription	Brain Angular Gyrus	brain
26	chr2:39250400-39295600	Weak transcription	NH-A	brain
27	chr2:39250400-39303000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr2:39250600-39279800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr2:39251000-39277000	Weak transcription	K562	blood
30	chr2:39251000-39293000	Weak transcription	HMEC	breast
31	chr2:39251600-39327200	Weak transcription	HUVEC	blood vessel
32	chr2:39252200-39279200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr2:39252400-39274000	Weak transcription	A549	lung
34	chr2:39252400-39292400	Weak transcription	NHEK	skin
35	chr2:39254200-39277200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr2:39255000-39299000	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr2:39255400-39278200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr2:39255600-39274600	Weak transcription	Brain Germinal Matrix	brain
39	chr2:39255800-39277600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr2:39258200-39277600	Weak transcription	Primary T cells from cord blood	blood
41	chr2:39258200-39293400	Weak transcription	Ovary	ovary
42	chr2:39258400-39270600	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr2:39258400-39273800	Weak transcription	Fetal Brain Female	brain
44	chr2:39258400-39274000	Weak transcription	Primary B cells from peripheral blood	blood
45	chr2:39258400-39276400	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr2:39258400-39282600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr2:39258400-39292800	Weak transcription	HSMMtube	muscle
48	chr2:39258400-39295800	Weak transcription	Colon Smooth Muscle	Colon
49	chr2:39258400-39299200	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr2:39258400-39322400	Weak transcription	Thymus	Thymus

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