Variant report

Variant	rs1377863
Chromosome Location	chr2:39238854-39238855
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	chr2:39237020..39239213-chr2:39240112..39243107,2	K562	blood:
2	chr2:39236974..39239611-chr2:39346618..39348424,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115904	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10153761	0.96[EUR][1000 genomes]
rs10165968	0.84[EUR][1000 genomes]
rs10166631	0.85[ASN][1000 genomes]
rs10166801	0.94[EUR][1000 genomes]
rs10169337	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10172085	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10184015	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10190377	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10194374	0.98[EUR][1000 genomes]
rs10204958	0.84[ASN][1000 genomes]
rs10205802	0.88[ASN][1000 genomes]
rs10206751	0.87[ASN][1000 genomes]
rs10439459	0.96[EUR][1000 genomes]
rs11124659	0.96[EUR][1000 genomes]
rs11124660	0.95[EUR][1000 genomes]
rs11674846	0.89[ASN][1000 genomes]
rs11691035	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11692687	0.89[EUR][1000 genomes]
rs12471731	0.85[ASN][1000 genomes]
rs12620003	0.84[EUR][1000 genomes]
rs12620071	0.93[EUR][1000 genomes]
rs12622969	0.82[EUR][1000 genomes]
rs13031871	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13033392	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1377860	0.93[EUR][1000 genomes]
rs1377861	0.93[EUR][1000 genomes]
rs1377864	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1454219	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1454226	0.96[EUR][1000 genomes]
rs1454227	0.84[EUR][1000 genomes]
rs1454228	0.91[EUR][1000 genomes]
rs1470914	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1470915	0.96[EUR][1000 genomes]
rs1840281	0.91[EUR][1000 genomes]
rs1947433	0.86[ASN][1000 genomes]
rs2060988	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2060989	0.93[EUR][1000 genomes]
rs2123876	0.93[EUR][1000 genomes]
rs2123879	0.85[EUR][1000 genomes]
rs2123881	0.96[EUR][1000 genomes]
rs2123882	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2373474	0.98[EUR][1000 genomes]
rs2373495	0.93[EUR][1000 genomes]
rs2373496	0.93[EUR][1000 genomes]
rs2373497	0.86[ASN][1000 genomes]
rs2888585	0.96[EUR][1000 genomes]
rs2924714	0.93[EUR][1000 genomes]
rs2969763	0.93[EUR][1000 genomes]
rs297121	0.93[EUR][1000 genomes]
rs297125	0.93[EUR][1000 genomes]
rs297128	0.93[EUR][1000 genomes]
rs297129	0.93[EUR][1000 genomes]
rs297130	0.93[EUR][1000 genomes]
rs297131	0.81[EUR][1000 genomes]
rs297132	0.82[EUR][1000 genomes]
rs297133	0.93[EUR][1000 genomes]
rs297134	0.82[EUR][1000 genomes]
rs297135	0.93[EUR][1000 genomes]
rs297136	0.82[EUR][1000 genomes]
rs297137	0.93[EUR][1000 genomes]
rs297139	0.93[EUR][1000 genomes]
rs297140	0.93[EUR][1000 genomes]
rs297141	0.93[EUR][1000 genomes]
rs297142	0.82[EUR][1000 genomes]
rs297143	0.93[EUR][1000 genomes]
rs297145	0.82[EUR][1000 genomes]
rs297147	0.82[EUR][1000 genomes]
rs297148	0.93[EUR][1000 genomes]
rs297149	0.93[EUR][1000 genomes]
rs297150	0.93[EUR][1000 genomes]
rs297151	0.80[EUR][1000 genomes]
rs297152	0.80[EUR][1000 genomes]
rs297153	0.93[EUR][1000 genomes]
rs297155	0.80[EUR][1000 genomes]
rs297156	0.80[EUR][1000 genomes]
rs297157	0.93[EUR][1000 genomes]
rs297158	0.95[EUR][1000 genomes]
rs297159	0.93[EUR][1000 genomes]
rs366840	0.82[EUR][1000 genomes]
rs378698	0.93[EUR][1000 genomes]
rs3796038	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs388958	0.82[EUR][1000 genomes]
rs4670272	0.93[EUR][1000 genomes]
rs4670902	0.85[ASN][1000 genomes]
rs4670904	0.89[ASN][1000 genomes]
rs4670905	0.93[EUR][1000 genomes]
rs57378308	0.95[EUR][1000 genomes]
rs58645871	0.85[EUR][1000 genomes]
rs59732351	0.95[EUR][1000 genomes]
rs61405040	0.93[EUR][1000 genomes]
rs6419600	0.82[EUR][1000 genomes]
rs6544186	0.87[ASN][1000 genomes]
rs6544188	0.85[ASN][1000 genomes]
rs6544189	0.82[ASN][1000 genomes]
rs6544191	0.93[EUR][1000 genomes]
rs6544194	0.80[EUR][1000 genomes]
rs6544195	0.80[EUR][1000 genomes]
rs6544197	0.93[EUR][1000 genomes]
rs6713281	0.96[EUR][1000 genomes]
rs6725356	0.98[EUR][1000 genomes]
rs6725644	0.98[EUR][1000 genomes]
rs6739807	0.85[ASN][1000 genomes]
rs6756184	0.93[EUR][1000 genomes]
rs6758330	0.84[ASN][1000 genomes]
rs72909662	0.95[EUR][1000 genomes]
rs7568552	0.91[EUR][1000 genomes]
rs7604229	0.88[ASN][1000 genomes]
rs7607509	0.88[ASN][1000 genomes]
rs9309031	0.95[EUR][1000 genomes]
rs970409	0.93[EUR][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
rs1377863	SOS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 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	chr2:39210400-39241600	Strong transcription	Adipose Nuclei	Adipose
3	chr2:39210400-39242600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr2:39210600-39242400	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr2:39211000-39247600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr2:39211600-39242000	Weak transcription	Stomach Mucosa	stomach
7	chr2:39211800-39239600	Strong transcription	Fetal Intestine Large	intestine
8	chr2:39213400-39242200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr2:39213400-39242600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:39213400-39251200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:39213400-39259800	Weak transcription	Right Ventricle	heart
12	chr2:39213800-39308000	Weak transcription	Pancreas	Pancrea
13	chr2:39217400-39241800	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr2:39217600-39242400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr2:39217600-39244200	Strong transcription	Primary B cells from cord blood	blood
16	chr2:39218800-39241200	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr2:39219000-39259200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr2:39219200-39244000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr2:39219400-39242600	Weak transcription	Brain Substantia Nigra	brain
20	chr2:39221000-39241200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr2:39225400-39241800	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr2:39225600-39241600	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr2:39225600-39241600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr2:39225600-39241600	Strong transcription	Placenta	Placenta
25	chr2:39225800-39241200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr2:39226200-39241600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:39227600-39303400	Weak transcription	Colonic Mucosa	Colon
28	chr2:39228000-39241200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr2:39229000-39251400	Weak transcription	Fetal Heart	heart
30	chr2:39229800-39239000	Weak transcription	K562	blood
31	chr2:39229800-39293000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:39230200-39240000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr2:39230200-39243600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr2:39230600-39239000	Weak transcription	NHDF-Ad	bronchial
35	chr2:39231000-39239800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr2:39231200-39241600	Strong transcription	HepG2	liver
37	chr2:39231600-39244400	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr2:39231800-39241600	Strong transcription	Dnd41	blood
39	chr2:39232000-39241200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr2:39232000-39241800	Strong transcription	Duodenum Mucosa	Duodenum
41	chr2:39232200-39242800	Strong transcription	Liver	Liver
42	chr2:39232400-39241000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr2:39232400-39242800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr2:39232600-39300000	Weak transcription	Brain Cingulate Gyrus	brain
45	chr2:39233000-39240800	Strong transcription	Fetal Brain Female	brain
46	chr2:39233800-39239800	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr2:39234400-39239400	Strong transcription	Brain Germinal Matrix	brain
48	chr2:39234400-39240400	Strong transcription	Primary hematopoietic stem cells	blood
49	chr2:39234400-39241200	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr2:39234400-39241200	Strong transcription	Rectal Mucosa Donor 29	rectum

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