Variant report

Variant	rs10166395
Chromosome Location	chr2:39211121-39211122
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	chr2:39210484..39212587-chr2:39214026..39216644,2	K562	blood:
3	chr2:39207664..39211487-chr2:39212740..39218159,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115904	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10165968	1.00[CEU][hapmap]
rs10166631	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10169337	0.80[CEU][hapmap]
rs10177250	1.00[CEU][hapmap]
rs10186762	0.80[ASN][1000 genomes]
rs10190377	1.00[CEU][hapmap];0.80[ASN][1000 genomes]
rs10201980	0.84[EUR][1000 genomes]
rs10205802	0.80[CEU][hapmap]
rs10206751	0.80[CEU][hapmap]
rs1037495	1.00[CEU][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1043793	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10779924	0.80[ASN][1000 genomes]
rs12471731	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12620003	1.00[CEU][hapmap]
rs12622969	1.00[CEU][hapmap]
rs13031871	0.88[CEU][hapmap]
rs13033392	0.80[ASN][1000 genomes]
rs1377864	1.00[CEU][hapmap]
rs1454221	0.81[ASN][1000 genomes]
rs1454222	0.80[ASN][1000 genomes]
rs1470914	1.00[CEU][hapmap]
rs1531021	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1869513	0.84[EUR][1000 genomes]
rs1947433	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2060988	0.80[CEU][hapmap]
rs2278913	0.84[EUR][1000 genomes]
rs2290445	0.81[ASN][1000 genomes]
rs2305516	0.84[EUR][1000 genomes]
rs297120	1.00[CEU][hapmap]
rs297124	1.00[CEU][hapmap]
rs297134	1.00[CEU][hapmap]
rs297136	1.00[CEU][hapmap]
rs297142	1.00[CEU][hapmap]
rs297144	1.00[CEU][hapmap]
rs297151	0.88[CEU][hapmap]
rs297152	0.88[CEU][hapmap]
rs297158	0.88[CEU][hapmap]
rs297160	0.85[CEU][hapmap]
rs371745	0.82[EUR][1000 genomes]
rs3796038	1.00[CEU][hapmap]
rs4670269	0.88[CEU][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4670901	0.84[EUR][1000 genomes]
rs4670902	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4670904	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6419600	1.00[CEU][hapmap]
rs6544184	0.84[EUR][1000 genomes]
rs6544186	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6704656	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6716101	0.84[EUR][1000 genomes]
rs672208	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6758330	0.80[CEU][hapmap]
rs7571052	0.84[EUR][1000 genomes]
rs7582918	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7607509	0.80[CEU][hapmap]
rs963730	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs963731	0.81[ASN][1000 genomes]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10166395	SOS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

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	chr2:39188200-39211800	Weak transcription	Fetal Lung	lung
6	chr2:39188400-39212000	Weak transcription	Fetal Muscle Leg	muscle
7	chr2:39188400-39212400	Weak transcription	Fetal Brain Female	brain
8	chr2:39189200-39212000	Weak transcription	Fetal Muscle Trunk	muscle
9	chr2:39194000-39213000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:39194400-39218600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr2:39194600-39212000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr2:39194600-39212800	Weak transcription	Spleen	Spleen
13	chr2:39195400-39212600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr2:39196600-39212600	Weak transcription	Aorta	Aorta
15	chr2:39197000-39225800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr2:39198600-39212600	Weak transcription	HSMMtube	muscle
17	chr2:39198800-39212000	Weak transcription	Fetal Stomach	stomach
18	chr2:39199600-39220000	Weak transcription	Brain Germinal Matrix	brain
19	chr2:39200000-39212000	Weak transcription	Primary T cells from cord blood	blood
20	chr2:39200000-39212200	Weak transcription	Pancreas	Pancrea
21	chr2:39200200-39212000	Weak transcription	Right Ventricle	heart
22	chr2:39200800-39227800	Weak transcription	Fetal Heart	heart
23	chr2:39201600-39211800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr2:39201600-39212800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr2:39201800-39212800	Weak transcription	Brain Angular Gyrus	brain
26	chr2:39201800-39218600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr2:39202000-39211400	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr2:39202000-39212600	Weak transcription	Ovary	ovary
29	chr2:39202000-39218800	Weak transcription	Brain Substantia Nigra	brain
30	chr2:39202000-39221800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr2:39202200-39212600	Weak transcription	Colon Smooth Muscle	Colon
32	chr2:39202400-39225600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr2:39202400-39228800	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr2:39202800-39217000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr2:39203600-39212000	Weak transcription	Lung	lung
36	chr2:39205200-39212800	Weak transcription	Left Ventricle	heart
37	chr2:39205400-39212600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr2:39205800-39212600	Weak transcription	Brain Anterior Caudate	brain
39	chr2:39205800-39242600	Weak transcription	Psoas Muscle	Psoas
40	chr2:39206000-39211400	Weak transcription	Fetal Kidney	kidney
41	chr2:39206000-39211600	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr2:39206000-39212800	Weak transcription	Thymus	Thymus
43	chr2:39206000-39235800	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr2:39206200-39212600	Weak transcription	HUVEC	blood vessel
45	chr2:39206400-39211200	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr2:39206400-39211600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr2:39206400-39212600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr2:39206600-39211800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr2:39206800-39212600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr2:39207000-39212400	Weak transcription	Brain Inferior Temporal Lobe	brain

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