Variant report

Variant	rs963730
Chromosome Location	chr2:39216773-39216774
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39214303..39217134-chr2:39220801..39223000,3	K562	blood:
2	chr2:39179721..39182563-chr2:39215625..39217531,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229692	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]
rs10166395	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10166631	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10166801	0.91[CHB][hapmap]
rs10169337	0.80[CEU][hapmap];0.83[JPT][hapmap]
rs10177250	1.00[CEU][hapmap];0.83[CHB][hapmap]
rs10183915	0.91[CHB][hapmap]
rs10184015	0.80[ASN][1000 genomes]
rs10186762	0.91[CHB][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10190377	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs10192250	1.00[CHB][hapmap]
rs10194374	0.91[CHB][hapmap]
rs10201980	0.91[CHB][hapmap]
rs10205802	0.80[CEU][hapmap];0.83[JPT][hapmap]
rs10206751	0.80[CEU][hapmap];0.83[JPT][hapmap]
rs1037495	1.00[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1043793	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]
rs12471731	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12620003	1.00[CEU][hapmap]
rs12622969	1.00[CEU][hapmap]
rs12712630	0.91[CHB][hapmap]
rs13031871	0.88[CEU][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs13033392	0.82[ASN][1000 genomes]
rs1377860	0.90[CHB][hapmap]
rs1377864	1.00[CEU][hapmap];0.86[AFR][1000 genomes]
rs1454221	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1454222	0.91[CHB][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1454223	1.00[CHB][hapmap]
rs1454226	0.91[CHB][hapmap]
rs1470914	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs1470915	0.91[CHB][hapmap]
rs1531021	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1869513	0.91[CHB][hapmap]
rs1947433	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2060987	0.83[CHB][hapmap]
rs2060988	0.80[CEU][hapmap]
rs2123879	0.90[CHB][hapmap]
rs2123881	0.91[CHB][hapmap]
rs2123882	0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs2168042	0.83[CHB][hapmap]
rs2278914	0.91[CHB][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2290445	1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2305516	0.91[CHB][hapmap]
rs2373495	0.91[CHB][hapmap]
rs2373496	0.90[CHB][hapmap]
rs2888585	0.83[CHB][hapmap]
rs297120	1.00[CEU][hapmap]
rs297124	1.00[CEU][hapmap]
rs297134	1.00[CEU][hapmap]
rs297135	0.83[CHB][hapmap]
rs297136	1.00[CEU][hapmap]
rs297142	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs297144	1.00[CEU][hapmap]
rs297148	0.89[CHB][hapmap]
rs297149	0.82[CHB][hapmap]
rs297150	0.83[CHB][hapmap]
rs297151	0.88[CEU][hapmap]
rs297152	0.88[CEU][hapmap]
rs297153	0.83[CHB][hapmap]
rs297158	0.88[CEU][hapmap];0.91[CHB][hapmap]
rs297160	0.85[CEU][hapmap]
rs3765058	0.91[CHB][hapmap]
rs378698	0.83[CHB][hapmap]
rs3796038	1.00[CEU][hapmap];0.86[AFR][1000 genomes]
rs4142729	1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs422854	0.91[CHB][hapmap]
rs4670269	0.88[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4670272	0.91[CHB][hapmap]
rs4670902	1.00[CEU][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4670903	0.91[CHB][hapmap];0.82[EUR][1000 genomes]
rs4670904	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6419600	1.00[CEU][hapmap]
rs6544183	0.83[CHB][hapmap]
rs6544185	0.83[CHB][hapmap]
rs6544186	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6544197	0.89[CHB][hapmap]
rs6704656	0.91[CHB][hapmap];0.80[ASN][1000 genomes]
rs6713281	0.91[CHB][hapmap]
rs6716101	0.91[CHB][hapmap]
rs672208	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6725356	0.91[CHB][hapmap]
rs6739568	0.91[CHB][hapmap]
rs6752850	0.82[EUR][1000 genomes]
rs6756184	0.91[CHB][hapmap]
rs6758330	0.80[CEU][hapmap];0.82[JPT][hapmap]
rs7571052	0.91[CHB][hapmap]
rs7577088	1.00[CHB][hapmap]
rs7582918	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7607509	0.80[CEU][hapmap];0.83[JPT][hapmap]
rs963731	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs9679498	0.91[CHB][hapmap];0.84[EUR][1000 genomes]
rs997344	0.91[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
rs963730	SOS1	Cis_1M	lymphoblastoid	RTeQTL
rs963730	SOS1	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39188000-39222400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:39194400-39218600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr2:39197000-39225800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr2:39199600-39220000	Weak transcription	Brain Germinal Matrix	brain
5	chr2:39200800-39227800	Weak transcription	Fetal Heart	heart
6	chr2:39201800-39218600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:39202000-39218800	Weak transcription	Brain Substantia Nigra	brain
8	chr2:39202000-39221800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr2:39202400-39225600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr2:39202400-39228800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr2:39202800-39217000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr2:39205800-39242600	Weak transcription	Psoas Muscle	Psoas
13	chr2:39206000-39235800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr2:39207600-39224400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:39209200-39222400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr2:39209200-39224000	Strong transcription	Placenta	Placenta
17	chr2:39209800-39224400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr2:39210000-39232000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:39210400-39216800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr2:39210400-39224800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr2:39210400-39233200	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr2:39210400-39241600	Strong transcription	Adipose Nuclei	Adipose
23	chr2:39210400-39242600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr2:39210600-39229400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr2:39210600-39242400	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr2:39210800-39218600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr2:39210800-39219200	Strong transcription	Fetal Thymus	thymus
28	chr2:39210800-39224800	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr2:39210800-39230200	Strong transcription	Dnd41	blood
30	chr2:39211000-39247600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr2:39211200-39224800	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr2:39211200-39228600	Strong transcription	HepG2	liver
33	chr2:39211400-39221200	Weak transcription	NHDF-Ad	bronchial
34	chr2:39211400-39237800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr2:39211600-39242000	Weak transcription	Stomach Mucosa	stomach
36	chr2:39211800-39231200	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr2:39211800-39239600	Strong transcription	Fetal Intestine Large	intestine
38	chr2:39212000-39216800	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr2:39213200-39218400	Weak transcription	HUVEC	blood vessel
40	chr2:39213200-39221400	Weak transcription	Colon Smooth Muscle	Colon
41	chr2:39213200-39221800	Weak transcription	HMEC	breast
42	chr2:39213400-39217200	Weak transcription	Primary hematopoietic stem cells	blood
43	chr2:39213400-39217400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr2:39213400-39217600	Weak transcription	HSMM	muscle
45	chr2:39213400-39218400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr2:39213400-39218400	Weak transcription	Colonic Mucosa	Colon
47	chr2:39213400-39218400	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr2:39213400-39218600	Weak transcription	Lung	lung
49	chr2:39213400-39218600	Weak transcription	Ovary	ovary
50	chr2:39213400-39218600	Weak transcription	A549	lung

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