Variant report

Variant	rs4670904
Chromosome Location	chr2:39228883-39228884
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 110 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10165968	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs10166395	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10166631	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10166801	0.83[CHB][hapmap]
rs10169337	0.80[CEU][hapmap]
rs10172085	0.85[ASN][1000 genomes]
rs10177250	1.00[CEU][hapmap];0.92[CHB][hapmap]
rs10183915	0.82[CHB][hapmap]
rs10184015	0.86[ASN][1000 genomes]
rs10186762	0.84[CHB][hapmap]
rs10190377	1.00[CEU][hapmap];0.89[JPT][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10192250	0.92[CHB][hapmap];0.81[ASN][1000 genomes]
rs10194374	0.84[CHB][hapmap]
rs10201980	1.00[CHB][hapmap]
rs10205802	0.80[CEU][hapmap]
rs10206751	0.80[CEU][hapmap];0.89[JPT][hapmap]
rs1037495	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.84[YRI][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1043793	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10439459	0.80[ASN][1000 genomes]
rs11124659	0.81[ASN][1000 genomes]
rs11674846	0.80[ASN][1000 genomes]
rs11691035	0.80[ASN][1000 genomes]
rs12471731	1.00[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12620003	1.00[CEU][hapmap]
rs12622969	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs12712630	0.84[CHB][hapmap]
rs13023273	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13031871	0.88[CEU][hapmap];0.88[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs13033392	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1377860	0.81[CHB][hapmap]
rs1377863	0.89[ASN][1000 genomes]
rs1377864	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1454219	0.82[ASN][1000 genomes]
rs1454222	1.00[CHB][hapmap]
rs1454223	0.92[CHB][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1454225	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1454226	0.84[CHB][hapmap]
rs1470914	1.00[CEU][hapmap];0.83[JPT][hapmap];0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1470915	0.83[CHB][hapmap]
rs1531021	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1869513	1.00[CHB][hapmap]
rs1947432	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1947433	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2060988	0.80[CEU][hapmap]
rs2123879	0.82[CHB][hapmap]
rs2123881	0.84[CHB][hapmap]
rs2123882	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2168042	0.92[CHB][hapmap]
rs2168043	0.83[JPT][hapmap]
rs2278914	0.83[CHB][hapmap]
rs2290445	0.92[CHB][hapmap]
rs2305516	1.00[CHB][hapmap]
rs2373474	0.81[ASN][1000 genomes]
rs2373495	0.84[CHB][hapmap]
rs2373496	0.81[CHB][hapmap]
rs2373497	0.88[JPT][hapmap]
rs2888585	0.92[CHB][hapmap]
rs297120	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs297124	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs297134	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs297135	0.92[CHB][hapmap]
rs297136	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs297142	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs297144	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs297148	1.00[CHB][hapmap]
rs297149	0.92[CHB][hapmap]
rs297150	0.92[CHB][hapmap]
rs297151	0.88[CEU][hapmap];0.88[JPT][hapmap]
rs297152	0.88[CEU][hapmap];0.89[JPT][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];0.85[JPT][hapmap]
rs3765058	1.00[CHB][hapmap]
rs378698	0.92[CHB][hapmap]
rs3796038	1.00[CEU][hapmap];0.84[JPT][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4142729	0.92[CHB][hapmap];0.81[ASN][1000 genomes]
rs422854	1.00[CHB][hapmap]
rs4643520	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4670269	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs4670270	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4670272	0.84[CHB][hapmap]
rs4670902	1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4670903	1.00[CHB][hapmap]
rs6419600	1.00[CEU][hapmap]
rs6544183	0.92[CHB][hapmap]
rs6544185	0.92[CHB][hapmap]
rs6544186	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6544197	0.90[CHB][hapmap]
rs6704656	1.00[CHB][hapmap]
rs6713281	0.83[CHB][hapmap];0.80[ASN][1000 genomes]
rs6716101	1.00[CHB][hapmap]
rs672208	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6725356	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs6725644	0.81[ASN][1000 genomes]
rs6739568	0.84[CHB][hapmap]
rs6756184	0.84[CHB][hapmap]
rs6758330	0.80[CEU][hapmap];0.82[JPT][hapmap]
rs7571052	1.00[CHB][hapmap]
rs7577088	0.92[CHB][hapmap];0.82[ASN][1000 genomes]
rs7582918	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7607509	0.80[CEU][hapmap]
rs9309031	0.81[ASN][1000 genomes]
rs963730	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs963731	0.92[CHB][hapmap]
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
rs4670904	SOS1	Cis_1M	lymphoblastoid	RTeQTL
rs4670904	SOS1	cis	multi-tissue	Pritchard

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39205800-39242600	Weak transcription	Psoas Muscle	Psoas
2	chr2:39206000-39235800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr2:39210000-39232000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:39210400-39233200	Strong transcription	Rectal Mucosa Donor 29	rectum
5	chr2:39210400-39241600	Strong transcription	Adipose Nuclei	Adipose
6	chr2:39210400-39242600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr2:39210600-39229400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr2:39210600-39242400	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr2:39210800-39230200	Strong transcription	Dnd41	blood
10	chr2:39211000-39247600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr2:39211400-39237800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr2:39211600-39242000	Weak transcription	Stomach Mucosa	stomach
13	chr2:39211800-39231200	Strong transcription	Rectal Mucosa Donor 31	rectum
14	chr2:39211800-39239600	Strong transcription	Fetal Intestine Large	intestine
15	chr2:39213400-39234400	Weak transcription	Gastric	stomach
16	chr2:39213400-39234400	Weak transcription	NHEK	skin
17	chr2:39213400-39242200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:39213400-39242600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:39213400-39251200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr2:39213400-39259800	Weak transcription	Right Ventricle	heart
21	chr2:39213800-39235000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr2:39213800-39235000	Weak transcription	Small Intestine	intestine
23	chr2:39213800-39308000	Weak transcription	Pancreas	Pancrea
24	chr2:39214200-39235400	Weak transcription	Hela-S3	cervix
25	chr2:39217400-39229000	Strong transcription	Liver	Liver
26	chr2:39217400-39241800	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr2:39217600-39230200	Strong transcription	Primary T cells from cord blood	blood
28	chr2:39217600-39231200	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr2:39217600-39234200	Strong transcription	Primary B cells from peripheral blood	blood
30	chr2:39217600-39242400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr2:39217600-39244200	Strong transcription	Primary B cells from cord blood	blood
32	chr2:39218800-39241200	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr2:39219000-39259200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr2:39219200-39244000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr2:39219400-39242600	Weak transcription	Brain Substantia Nigra	brain
36	chr2:39220400-39233000	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr2:39220600-39237000	Strong transcription	Fetal Thymus	thymus
38	chr2:39221000-39241200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr2:39223400-39230000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr2:39223600-39235000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr2:39224400-39230600	Strong transcription	Duodenum Mucosa	Duodenum
42	chr2:39224400-39233800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr2:39225000-39229800	Strong transcription	Fetal Kidney	kidney
44	chr2:39225000-39230200	Strong transcription	Thymus	Thymus
45	chr2:39225000-39231200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr2:39225000-39231400	Strong transcription	Primary hematopoietic stem cells	blood
47	chr2:39225000-39233200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr2:39225200-39233200	Strong transcription	Fetal Muscle Trunk	muscle
49	chr2:39225400-39241800	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr2:39225600-39229200	Strong transcription	Brain Anterior Caudate	brain

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