Variant report

Variant	rs1043793
Chromosome Location	chr2:39209047-39209048
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39204550..39206116-chr2:39208967..39211436,2	K562	blood:
2	chr2:39201852..39204298-chr2:39208279..39210367,3	K562	blood:
3	chr2:39207664..39211487-chr2:39212740..39218159,6	MCF-7	breast:
4	chr2:39201485..39204258-chr2:39207506..39209401,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115904	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10165968	1.00[CEU][hapmap];0.90[GIH][hapmap]
rs10166395	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10166631	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10166801	0.83[CHB][hapmap]
rs10169337	0.80[CEU][hapmap]
rs10177250	1.00[CEU][hapmap];0.92[CHB][hapmap]
rs10183915	0.82[CHB][hapmap]
rs10186762	0.84[CHB][hapmap]
rs10190377	1.00[CEU][hapmap]
rs10192250	0.92[CHB][hapmap]
rs10194374	0.84[CHB][hapmap]
rs10201980	1.00[CHB][hapmap];0.90[GIH][hapmap];0.81[ASN][1000 genomes]
rs10205802	0.80[CEU][hapmap]
rs10206751	0.80[CEU][hapmap];0.83[JPT][hapmap]
rs1037495	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10779924	0.83[ASN][1000 genomes]
rs12471731	0.94[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.87[LWK][hapmap];0.89[MKK][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12620003	1.00[CEU][hapmap]
rs12622969	1.00[CEU][hapmap]
rs12712630	0.84[CHB][hapmap]
rs13031871	0.94[ASW][hapmap];0.88[CEU][hapmap];0.93[GIH][hapmap];0.80[LWK][hapmap];0.88[MKK][hapmap];0.85[YRI][hapmap]
rs1377860	0.81[CHB][hapmap]
rs1377864	1.00[CEU][hapmap]
rs1454221	0.80[ASN][1000 genomes]
rs1454222	1.00[CHB][hapmap]
rs1454223	0.92[CHB][hapmap]
rs1454226	0.84[CHB][hapmap]
rs1470914	1.00[CEU][hapmap]
rs1470915	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs1531021	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1869513	1.00[CHB][hapmap];0.86[GIH][hapmap];0.82[ASN][1000 genomes]
rs1947433	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2060988	0.80[CEU][hapmap];0.83[GIH][hapmap]
rs2123879	0.82[CHB][hapmap]
rs2123881	0.84[CHB][hapmap]
rs2168042	0.92[CHB][hapmap]
rs2168044	0.81[ASN][1000 genomes]
rs2278914	0.83[CHB][hapmap]
rs2290445	0.92[CHB][hapmap];0.80[ASN][1000 genomes]
rs2305516	1.00[CHB][hapmap];0.93[GIH][hapmap]
rs2373495	0.84[CHB][hapmap]
rs2373496	0.81[CHB][hapmap]
rs2373497	0.81[GIH][hapmap]
rs2888585	0.92[CHB][hapmap]
rs297120	1.00[CEU][hapmap];0.90[GIH][hapmap]
rs297124	1.00[CEU][hapmap];0.90[GIH][hapmap]
rs297134	1.00[CEU][hapmap]
rs297135	0.92[CHB][hapmap]
rs297136	1.00[CEU][hapmap]
rs297142	1.00[CEU][hapmap];0.90[GIH][hapmap]
rs297144	1.00[CEU][hapmap]
rs297148	1.00[CHB][hapmap]
rs297149	0.92[CHB][hapmap]
rs297150	0.92[CHB][hapmap];0.86[GIH][hapmap]
rs297151	0.88[CEU][hapmap];0.90[GIH][hapmap]
rs297152	0.88[CEU][hapmap]
rs297153	0.92[CHB][hapmap]
rs297158	0.88[CEU][hapmap];0.84[CHB][hapmap]
rs297159	0.84[CHB][hapmap]
rs297160	0.85[CEU][hapmap];0.90[CHB][hapmap]
rs3765058	1.00[CHB][hapmap];0.89[GIH][hapmap]
rs378698	0.92[CHB][hapmap]
rs3796038	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs4142729	0.92[CHB][hapmap];0.82[GIH][hapmap]
rs422854	1.00[CHB][hapmap]
rs4670269	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4670272	0.84[CHB][hapmap]
rs4670902	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4670903	1.00[CHB][hapmap]
rs4670904	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6419600	1.00[CEU][hapmap]
rs6544183	0.92[CHB][hapmap];0.86[GIH][hapmap]
rs6544185	0.92[CHB][hapmap];0.89[GIH][hapmap]
rs6544186	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6544197	0.90[CHB][hapmap]
rs6704656	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs6713281	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs6716101	1.00[CHB][hapmap]
rs672208	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6725356	0.83[CHB][hapmap]
rs6739568	0.84[CHB][hapmap]
rs6756184	0.84[CHB][hapmap]
rs6758330	0.80[CEU][hapmap];0.84[GIH][hapmap]
rs7571052	1.00[CHB][hapmap];0.89[GIH][hapmap]
rs7577088	0.92[CHB][hapmap];0.83[GIH][hapmap]
rs7582918	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7594644	0.82[ASN][1000 genomes]
rs7607509	0.80[CEU][hapmap]
rs963730	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs963731	0.92[CHB][hapmap];0.80[ASN][1000 genomes]
rs9679498	0.83[CHB][hapmap]
rs997344	0.84[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1043793	SOS1	Cis_1M	lymphoblastoid	RTeQTL
rs1043793	SOS1	cis	multi-tissue	Pritchard

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39188000-39212400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr2:39188000-39212600	Weak transcription	Gastric	stomach
3	chr2:39188000-39213000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:39188000-39222400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr2:39188200-39210800	Weak transcription	HMEC	breast
6	chr2:39188200-39211800	Weak transcription	Fetal Lung	lung
7	chr2:39188400-39212000	Weak transcription	Fetal Muscle Leg	muscle
8	chr2:39188400-39212400	Weak transcription	Fetal Brain Female	brain
9	chr2:39189200-39212000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr2:39194000-39213000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:39194400-39218600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr2:39194600-39212000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr2:39194600-39212800	Weak transcription	Spleen	Spleen
14	chr2:39195200-39210400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr2:39195400-39212600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr2:39196600-39212600	Weak transcription	Aorta	Aorta
17	chr2:39197000-39225800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr2:39197200-39211000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr2:39197400-39210800	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr2:39198600-39212600	Weak transcription	HSMMtube	muscle
21	chr2:39198800-39212000	Weak transcription	Fetal Stomach	stomach
22	chr2:39199200-39211000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr2:39199600-39220000	Weak transcription	Brain Germinal Matrix	brain
24	chr2:39200000-39212000	Weak transcription	Primary T cells from cord blood	blood
25	chr2:39200000-39212200	Weak transcription	Pancreas	Pancrea
26	chr2:39200200-39212000	Weak transcription	Right Ventricle	heart
27	chr2:39200600-39210800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr2:39200800-39227800	Weak transcription	Fetal Heart	heart
29	chr2:39201200-39210600	Weak transcription	HSMM	muscle
30	chr2:39201600-39211800	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr2:39201600-39212800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr2:39201800-39212800	Weak transcription	Brain Angular Gyrus	brain
33	chr2:39201800-39218600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr2:39202000-39210400	Weak transcription	Adipose Nuclei	Adipose
35	chr2:39202000-39211400	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr2:39202000-39212600	Weak transcription	Ovary	ovary
37	chr2:39202000-39218800	Weak transcription	Brain Substantia Nigra	brain
38	chr2:39202000-39221800	Weak transcription	Rectal Smooth Muscle	rectum
39	chr2:39202200-39210400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr2:39202200-39210800	Weak transcription	Brain Hippocampus Middle	brain
41	chr2:39202200-39212600	Weak transcription	Colon Smooth Muscle	Colon
42	chr2:39202400-39210800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:39202400-39225600	Weak transcription	Brain Cingulate Gyrus	brain
44	chr2:39202400-39228800	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr2:39202800-39217000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr2:39203600-39212000	Weak transcription	Lung	lung
47	chr2:39203800-39210200	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr2:39204000-39210400	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr2:39205200-39212800	Weak transcription	Left Ventricle	heart
50	chr2:39205400-39210200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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