Variant report

Variant	rs13031871
Chromosome Location	chr2:39252851-39252852
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr2:39252794-39253097	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39245988..39251682-chr2:39252776..39257874,7	K562	blood:

Variant related genes	Relation type
SOS1	TF binding region
ENSG00000115904	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10153761	0.80[EUR][1000 genomes]
rs10165968	0.88[CEU][hapmap];0.87[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs10166395	0.88[CEU][hapmap]
rs10166631	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10166801	0.82[EUR][1000 genomes]
rs10169337	0.81[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10172085	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10172714	0.86[GIH][hapmap]
rs10177250	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs10184015	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10190377	0.88[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10200058	0.86[EUR][1000 genomes]
rs10201980	0.93[CHD][hapmap];0.90[GIH][hapmap]
rs10204958	0.81[ASN][1000 genomes]
rs10205802	0.81[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs10206751	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1037495	0.88[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap];0.89[YRI][hapmap]
rs1043793	0.94[ASW][hapmap];0.88[CEU][hapmap];0.93[GIH][hapmap];0.80[LWK][hapmap];0.88[MKK][hapmap];0.85[YRI][hapmap]
rs10439459	0.80[EUR][1000 genomes]
rs11124659	0.80[EUR][1000 genomes]
rs11674846	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11691035	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11692687	0.80[EUR][1000 genomes]
rs12471731	1.00[ASW][hapmap];0.88[CEU][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.93[LWK][hapmap];0.90[MEX][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12620003	0.85[CEU][hapmap];0.88[JPT][hapmap];0.87[EUR][1000 genomes]
rs12622969	0.88[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs13033392	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1377860	0.83[CHD][hapmap]
rs1377863	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1377864	0.88[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1454219	0.88[ASN][1000 genomes]
rs1454223	0.87[CHD][hapmap]
rs1454226	0.80[EUR][1000 genomes]
rs1454227	0.93[EUR][1000 genomes]
rs1454228	0.85[EUR][1000 genomes]
rs1470914	0.88[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1470915	0.93[CHD][hapmap];0.93[GIH][hapmap];0.80[EUR][1000 genomes]
rs1840281	0.85[EUR][1000 genomes]
rs1869513	0.90[CHD][hapmap];0.86[GIH][hapmap]
rs1947433	0.85[ASN][1000 genomes]
rs2060987	0.83[CHD][hapmap]
rs2060988	0.86[CHB][hapmap];0.80[CHD][hapmap];0.90[GIH][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2123876	0.84[EUR][1000 genomes]
rs2123881	0.80[EUR][1000 genomes]
rs2123882	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2168043	0.80[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap]
rs2278914	0.87[CHD][hapmap]
rs2290445	0.84[CHD][hapmap]
rs2305516	0.80[CHD][hapmap];0.93[GIH][hapmap]
rs2373495	0.84[EUR][1000 genomes]
rs2373496	0.84[EUR][1000 genomes]
rs2373497	0.87[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.87[ASN][1000 genomes]
rs2888585	0.80[EUR][1000 genomes]
rs297120	0.88[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs297124	0.88[CEU][hapmap];0.81[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes]
rs297127	0.86[EUR][1000 genomes]
rs297131	0.90[EUR][1000 genomes]
rs297132	0.92[EUR][1000 genomes]
rs297134	0.88[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs297136	0.88[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs297142	0.88[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes]
rs297144	0.88[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs297145	0.89[EUR][1000 genomes]
rs297147	0.89[EUR][1000 genomes]
rs297150	0.93[GIH][hapmap]
rs297151	0.87[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs297152	0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs297155	0.86[EUR][1000 genomes]
rs297156	0.87[EUR][1000 genomes]
rs297160	0.84[JPT][hapmap]
rs297161	0.86[EUR][1000 genomes]
rs366840	0.89[EUR][1000 genomes]
rs3765058	0.81[CHD][hapmap];0.96[GIH][hapmap]
rs3796038	0.88[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs388958	0.89[EUR][1000 genomes]
rs4142729	0.82[GIH][hapmap]
rs4670269	0.84[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap]
rs4670272	0.84[EUR][1000 genomes]
rs4670902	0.88[CEU][hapmap];0.89[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4670904	0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6419600	0.86[CEU][hapmap];0.89[EUR][1000 genomes]
rs6544183	0.93[GIH][hapmap]
rs6544185	0.96[GIH][hapmap]
rs6544186	0.89[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6544188	0.86[ASN][1000 genomes]
rs6544189	0.83[ASN][1000 genomes]
rs6713281	0.93[CHD][hapmap];0.93[GIH][hapmap];0.80[EUR][1000 genomes]
rs6725356	0.87[CHD][hapmap];0.86[GIH][hapmap]
rs6726833	0.83[EUR][1000 genomes]
rs6739807	0.86[ASN][1000 genomes]
rs6756184	0.84[EUR][1000 genomes]
rs6758330	0.81[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7568552	0.82[EUR][1000 genomes]
rs7571052	0.81[CHD][hapmap];0.96[GIH][hapmap]
rs7577088	0.87[CHD][hapmap];0.90[GIH][hapmap]
rs7604229	0.89[ASN][1000 genomes]
rs7607509	0.81[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs963730	0.88[CEU][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.80[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs13031871	DHX57	cis	parietal	SCAN
rs13031871	SOS1	Cis_1M	lymphoblastoid	RTeQTL
rs13031871	SOS1	cis	multi-tissue	Pritchard
rs13031871	SOS1	cis	lymphoblastoid	seeQTL
rs13031871	ATL2	cis	parietal	SCAN
rs13031871	TMEM178	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39213400-39259800	Weak transcription	Right Ventricle	heart
2	chr2:39213800-39308000	Weak transcription	Pancreas	Pancrea
3	chr2:39219000-39259200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:39227600-39303400	Weak transcription	Colonic Mucosa	Colon
5	chr2:39229800-39293000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr2:39232600-39300000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr2:39235400-39312000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:39235600-39259800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:39235600-39259800	Weak transcription	Spleen	Spleen
10	chr2:39235600-39293200	Weak transcription	Fetal Brain Male	brain
11	chr2:39235600-39295800	Weak transcription	NHLF	lung
12	chr2:39235600-39298200	Weak transcription	Small Intestine	intestine
13	chr2:39235600-39327800	Weak transcription	Esophagus	oesophagus
14	chr2:39235800-39257800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:39235800-39284000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr2:39235800-39293600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr2:39236000-39260000	Weak transcription	Hela-S3	cervix
18	chr2:39236000-39295600	Weak transcription	Aorta	Aorta
19	chr2:39236000-39295800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr2:39236000-39305600	Weak transcription	Gastric	stomach
21	chr2:39236200-39305600	Weak transcription	Lung	lung
22	chr2:39236400-39263400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr2:39237000-39260200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr2:39237600-39257600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr2:39238400-39256400	Weak transcription	Fetal Intestine Small	intestine
26	chr2:39238400-39260600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr2:39238600-39256400	Weak transcription	Fetal Stomach	stomach
28	chr2:39239400-39254600	Weak transcription	Brain Germinal Matrix	brain
29	chr2:39240800-39257600	Weak transcription	Stomach Smooth Muscle	stomach
30	chr2:39240800-39257800	Weak transcription	Fetal Brain Female	brain
31	chr2:39240800-39262600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr2:39240800-39299200	Weak transcription	Brain Hippocampus Middle	brain
33	chr2:39241200-39256600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr2:39241200-39259800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr2:39241600-39276400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr2:39241600-39292800	Weak transcription	GM12878-XiMat	blood
37	chr2:39243200-39299600	Weak transcription	Brain Substantia Nigra	brain
38	chr2:39244600-39295400	Weak transcription	Rectal Smooth Muscle	rectum
39	chr2:39244800-39257800	Weak transcription	Colon Smooth Muscle	Colon
40	chr2:39246200-39259600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr2:39246600-39274000	Weak transcription	Fetal Kidney	kidney
42	chr2:39246800-39254400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr2:39246800-39257800	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr2:39248000-39257600	Weak transcription	Left Ventricle	heart
45	chr2:39248000-39257800	Weak transcription	HSMMtube	muscle
46	chr2:39249600-39262000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr2:39250000-39282200	Weak transcription	Brain Anterior Caudate	brain
48	chr2:39250000-39292800	Weak transcription	Psoas Muscle	Psoas
49	chr2:39250200-39254600	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr2:39250200-39256400	Weak transcription	Thymus	Thymus

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