Variant report

Variant	rs7583010
Chromosome Location	chr2:39261251-39261252
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38976851..38978644-chr2:39259210..39261593,2	K562	blood:
2	chr2:39257934..39259870-chr2:39260403..39263004,2	K562	blood:
3	chr2:39247075..39249060-chr2:39260609..39262656,2	K562	blood:

Variant related genes	Relation type
ENSG00000115875	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10169337	0.83[YRI][hapmap]
rs10173380	0.90[ASN][1000 genomes]
rs10184046	1.00[CEU][hapmap]
rs10184855	1.00[CEU][hapmap]
rs10186842	1.00[CEU][hapmap]
rs10189440	1.00[CEU][hapmap]
rs10199955	1.00[CEU][hapmap]
rs10205802	0.83[YRI][hapmap]
rs10207187	1.00[CEU][hapmap]
rs10495883	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13394446	1.00[CEU][hapmap]
rs13411756	1.00[CEU][hapmap]
rs13416725	1.00[CEU][hapmap]
rs1451278	1.00[CEU][hapmap]
rs17023149	1.00[CEU][hapmap]
rs17023214	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs17023241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17023272	0.82[JPT][hapmap];0.95[ASN][1000 genomes]
rs17023292	1.00[CEU][hapmap]
rs1901290	1.00[CEU][hapmap]
rs2373466	1.00[CEU][hapmap]
rs2373472	1.00[CEU][hapmap]
rs297144	0.83[YRI][hapmap]
rs3099938	1.00[CEU][hapmap]
rs3099947	1.00[CEU][hapmap]
rs3112157	1.00[CEU][hapmap]
rs3112158	1.00[CEU][hapmap]
rs3112160	1.00[CEU][hapmap]
rs3112164	1.00[CEU][hapmap]
rs3112176	1.00[CEU][hapmap]
rs41280639	0.85[ASN][1000 genomes]
rs59988245	0.95[ASN][1000 genomes]
rs61049772	0.95[ASN][1000 genomes]
rs61521176	0.90[ASN][1000 genomes]
rs6544200	1.00[CEU][hapmap]
rs6709646	1.00[ASN][1000 genomes]
rs6729359	1.00[ASN][1000 genomes]
rs6758330	0.83[YRI][hapmap]
rs72918721	1.00[ASN][1000 genomes]
rs7559174	0.82[JPT][hapmap]
rs7564481	1.00[CEU][hapmap]
rs7565814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7571608	1.00[CEU][hapmap]
rs7571719	1.00[CEU][hapmap]
rs7574214	1.00[CEU][hapmap]
rs7589303	1.00[CEU][hapmap]
rs7599990	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs9678084	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]

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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7583010	SOS1	cis	multi-tissue	Pritchard
rs7583010	SOS1	cis	lymphoblastoid	seeQTL

Chromatin state (count:117 , 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	chr2:39236400-39263400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr2:39240800-39262600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr2:39240800-39299200	Weak transcription	Brain Hippocampus Middle	brain
19	chr2:39241600-39276400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr2:39241600-39292800	Weak transcription	GM12878-XiMat	blood
21	chr2:39243200-39299600	Weak transcription	Brain Substantia Nigra	brain
22	chr2:39244600-39295400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr2:39246600-39274000	Weak transcription	Fetal Kidney	kidney
24	chr2:39249600-39262000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr2:39250000-39282200	Weak transcription	Brain Anterior Caudate	brain
26	chr2:39250000-39292800	Weak transcription	Psoas Muscle	Psoas
27	chr2:39250200-39295200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr2:39250200-39313600	Weak transcription	Brain Angular Gyrus	brain
29	chr2:39250400-39262200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr2:39250400-39295600	Weak transcription	NH-A	brain
31	chr2:39250400-39303000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr2:39250600-39279800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr2:39251000-39277000	Weak transcription	K562	blood
34	chr2:39251000-39293000	Weak transcription	HMEC	breast
35	chr2:39251600-39327200	Weak transcription	HUVEC	blood vessel
36	chr2:39252200-39279200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr2:39252400-39274000	Weak transcription	A549	lung
38	chr2:39252400-39292400	Weak transcription	NHEK	skin
39	chr2:39253600-39262000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr2:39253800-39262400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:39254200-39277200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr2:39254600-39261400	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr2:39254600-39262600	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr2:39255000-39299000	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr2:39255200-39261600	Strong transcription	Adipose Nuclei	Adipose
46	chr2:39255200-39262000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr2:39255400-39278200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr2:39255600-39262000	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr2:39255600-39262200	Strong transcription	Fetal Intestine Large	intestine
50	chr2:39255600-39262600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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