Variant report

Variant	rs6544224
Chromosome Location	chr2:39620989-39620990
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39619324..39621910-chr2:39662875..39665257,2	K562	blood:

Variant related genes	Relation type
ENSG00000011566	Chromatin interaction
ENSG00000231312	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10153665	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs10170424	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10170617	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10172736	0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[EUR][1000 genomes]
rs10173556	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10173722	0.84[AFR][1000 genomes]
rs10175038	0.84[EUR][1000 genomes]
rs10190069	0.85[EUR][1000 genomes]
rs10193636	0.88[CHB][hapmap]
rs10195629	0.81[EUR][1000 genomes]
rs1035232	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10865149	0.86[EUR][1000 genomes]
rs10865150	1.00[CEU][hapmap];0.81[YRI][hapmap];0.92[EUR][1000 genomes]
rs10865152	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11124668	0.84[EUR][1000 genomes]
rs11124673	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11124676	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs11124679	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1125839	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11688728	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1211996	0.87[EUR][1000 genomes]
rs12622941	0.87[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12712636	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1468902	0.82[EUR][1000 genomes]
rs17023837	0.91[EUR][1000 genomes]
rs1861735	0.88[EUR][1000 genomes]
rs1922827	0.87[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2005892	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2160661	0.90[AFR][1000 genomes]
rs2178762	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2193422	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2373534	0.87[CEU][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2373535	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2542008	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2888594	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2888598	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3755177	0.88[EUR][1000 genomes]
rs3755178	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs3770663	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs3770670	0.88[EUR][1000 genomes]
rs3770675	0.83[EUR][1000 genomes]
rs3770678	0.84[EUR][1000 genomes]
rs3815594	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs3887311	0.83[AMR][1000 genomes]
rs6544213	0.84[EUR][1000 genomes]
rs6544220	0.80[EUR][1000 genomes]
rs6544222	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6712274	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6712921	0.83[EUR][1000 genomes]
rs6718134	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6725938	0.84[EUR][1000 genomes]
rs6732611	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6736700	0.83[EUR][1000 genomes]
rs6741019	0.84[EUR][1000 genomes]
rs6742170	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6743041	0.87[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6753323	0.92[EUR][1000 genomes]
rs6756183	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs6760382	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7573535	0.86[CHB][hapmap]
rs7574250	0.83[AMR][1000 genomes]
rs7578136	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7579414	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7582160	0.81[YRI][hapmap]
rs759589	0.86[EUR][1000 genomes]
rs7600014	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs7600046	0.88[EUR][1000 genomes]
rs7601700	0.82[CEU][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7603337	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7604047	0.82[EUR][1000 genomes]
rs7608153	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9309039	0.90[CHB][hapmap];0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv581494	chr2:39277851-39626388	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	esv1827292	chr2:39385155-39675339	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv1812828	chr2:39396457-39675339	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6544224	SOS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39588000-39630400	Weak transcription	Placenta	Placenta
2	chr2:39591800-39621400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:39603200-39638400	Weak transcription	Hela-S3	cervix
4	chr2:39603400-39625000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr2:39603400-39626800	Weak transcription	Primary T cells from cord blood	blood
6	chr2:39607000-39626800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:39607400-39624800	Weak transcription	Stomach Mucosa	stomach
8	chr2:39607600-39643400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr2:39608000-39622800	Weak transcription	Fetal Kidney	kidney
10	chr2:39608400-39621000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr2:39608400-39626200	Weak transcription	Brain Substantia Nigra	brain
12	chr2:39609200-39621600	Weak transcription	Lung	lung
13	chr2:39609400-39621200	Weak transcription	Brain Angular Gyrus	brain
14	chr2:39609400-39621200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr2:39609400-39621600	Weak transcription	HSMM	muscle
16	chr2:39609600-39621200	Weak transcription	Brain Hippocampus Middle	brain
17	chr2:39609600-39621400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr2:39609600-39621600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr2:39609600-39621600	Weak transcription	NH-A	brain
20	chr2:39609600-39621600	Weak transcription	Osteobl	bone
21	chr2:39609600-39626400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr2:39610000-39621200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:39610200-39621800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr2:39610200-39626400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr2:39613000-39621400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr2:39613400-39621200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:39613600-39621600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:39613600-39621600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr2:39613800-39630600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr2:39614000-39628000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr2:39614800-39621600	Weak transcription	Pancreas	Pancrea
32	chr2:39615600-39621400	Weak transcription	Stomach Smooth Muscle	stomach
33	chr2:39615800-39621200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr2:39615800-39626800	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr2:39616000-39621200	Weak transcription	Aorta	Aorta
36	chr2:39616000-39622200	Weak transcription	Fetal Stomach	stomach
37	chr2:39616000-39626400	Weak transcription	Gastric	stomach
38	chr2:39616800-39621200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr2:39617600-39621200	Weak transcription	Fetal Heart	heart
40	chr2:39617600-39626200	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr2:39617600-39626400	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr2:39617800-39621200	Weak transcription	Rectal Smooth Muscle	rectum
43	chr2:39617800-39621200	Weak transcription	NHLF	lung
44	chr2:39617800-39621400	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr2:39617800-39621400	Weak transcription	NHDF-Ad	bronchial
46	chr2:39617800-39621600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr2:39617800-39621600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr2:39617800-39621600	Weak transcription	Ovary	ovary
49	chr2:39617800-39626200	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr2:39617800-39628200	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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