Variant report

Variant	rs2271923
Chromosome Location	chr4:57272620-57272621
allele	A/G
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	CEBPB	chr4:57272388-57272697	HepG2	liver:	n/a	n/a
2	CEBPB	chr4:57272387-57272708	K562	blood:	n/a	n/a
3	CEBPB	chr4:57272354-57272660	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:57265970..57269312-chr4:57270989..57273638,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000268171	TF binding region
ENSG00000128059	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10434444	0.90[YRI][hapmap]
rs10434445	0.84[EUR][1000 genomes]
rs1060472	1.00[CEU][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11133442	1.00[CEU][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11133443	0.80[TSI][hapmap]
rs12498340	0.81[MKK][hapmap];0.83[TSI][hapmap];0.81[YRI][hapmap]
rs12501334	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12501502	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12503412	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12504291	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs12510712	0.81[EUR][1000 genomes]
rs12511770	0.81[AMR][1000 genomes]
rs1401907	0.91[JPT][hapmap]
rs1474179	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1520026	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1520030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17086696	0.83[TSI][hapmap];0.81[YRI][hapmap]
rs1967559	1.00[CEU][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1983378	0.90[YRI][hapmap]
rs2049087	0.91[MEX][hapmap]
rs28866881	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3796541	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796548	0.80[TSI][hapmap]
rs4346704	0.80[AMR][1000 genomes]
rs4493603	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4864579	0.81[YRI][hapmap]
rs4864583	1.00[CEU][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs5010012	0.91[CEU][hapmap];0.89[YRI][hapmap];0.89[EUR][1000 genomes]
rs56392224	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58151706	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs66810706	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6819534	0.91[MEX][hapmap]
rs6820314	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6821301	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs6829250	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6832797	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6834696	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6836118	0.80[TSI][hapmap]
rs6846895	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6855041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7664841	1.00[CEU][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes]
rs7671868	0.95[JPT][hapmap]
rs8340	0.81[LWK][hapmap];0.83[TSI][hapmap];0.81[YRI][hapmap]
rs9996593	0.87[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv4347	chr4:57261404-57280595	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv1801975	chr4:57267406-57297335	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2271923	AASDH	cis	parietal	SCAN
rs2271923	PPAT	cis	lymphoblastoid	seeQTL
rs2271923	SRP72	cis	cerebellum	SCAN
rs2271923	AASDH	cis	cerebellum	SCAN
rs2271923	SRP72	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57254200-57273800	Weak transcription	Spleen	Spleen
2	chr4:57254400-57273600	Weak transcription	Pancreas	Pancrea
3	chr4:57254600-57276400	Weak transcription	Psoas Muscle	Psoas
4	chr4:57254600-57280200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr4:57254800-57273200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr4:57254800-57275200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr4:57254800-57275400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr4:57254800-57276400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr4:57254800-57276400	Weak transcription	Right Ventricle	heart
10	chr4:57254800-57276600	Weak transcription	Left Ventricle	heart
11	chr4:57254800-57287600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr4:57255200-57275600	Weak transcription	NHLF	lung
13	chr4:57255200-57276400	Weak transcription	Colon Smooth Muscle	Colon
14	chr4:57255200-57276600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr4:57255200-57276600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr4:57255200-57276600	Weak transcription	Brain Substantia Nigra	brain
17	chr4:57255400-57276400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr4:57255600-57275600	Weak transcription	Fetal Brain Female	brain
19	chr4:57255800-57276600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr4:57256000-57274200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr4:57256000-57276400	Weak transcription	Brain Hippocampus Middle	brain
22	chr4:57256200-57276600	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr4:57256400-57276600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr4:57257600-57274200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:57258400-57274200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr4:57259000-57274000	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr4:57259400-57275600	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr4:57260200-57274200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr4:57260600-57273000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr4:57260800-57274200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr4:57261000-57273200	Strong transcription	Dnd41	blood
32	chr4:57261200-57273000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr4:57262000-57273400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr4:57264000-57274000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr4:57264200-57274000	Strong transcription	GM12878-XiMat	blood
36	chr4:57264200-57290200	Weak transcription	Esophagus	oesophagus
37	chr4:57264400-57276400	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr4:57264800-57273000	Weak transcription	Thymus	Thymus
39	chr4:57264800-57301000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr4:57265000-57301000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr4:57265200-57275600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr4:57265400-57273400	Strong transcription	K562	blood
43	chr4:57266200-57272800	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr4:57266200-57273200	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr4:57266800-57273000	Strong transcription	HepG2	liver
46	chr4:57267200-57275600	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr4:57267400-57273000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr4:57267400-57274800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr4:57267400-57275400	Weak transcription	NHDF-Ad	bronchial
50	chr4:57267600-57275600	Weak transcription	Brain Cingulate Gyrus	brain

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