Variant report

Variant	rs6571920
Chromosome Location	chr14:39793554-39793555
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10136852	0.80[ASW][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.86[MEX][hapmap]
rs10139612	0.86[CHB][hapmap]
rs10145517	0.81[JPT][hapmap]
rs10145518	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs10148141	0.81[EUR][1000 genomes]
rs10149896	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10872918	0.80[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs17109068	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap]
rs17109118	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17693410	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2274397	0.80[ASW][hapmap];0.93[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28718785	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28776502	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4328353	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4393482	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs4636812	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4899200	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs4902520	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4902542	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56126634	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61398943	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62000665	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs62000689	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62000717	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7141921	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs7148572	0.80[ASW][hapmap];0.93[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[MKK][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7149197	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7150685	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7159130	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs72675418	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8016293	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8017650	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap]
rs8018486	0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8019758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8022515	0.96[AFR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037183	chr14:39736939-39949233	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv542048	chr14:39736939-39949233	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6571920	BRMS1L	cis	parietal	SCAN
rs6571920	FOXA1	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39738200-39813800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr14:39752600-39808200	Weak transcription	Stomach Mucosa	stomach
3	chr14:39755600-39797200	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr14:39756200-39828400	Weak transcription	Brain Germinal Matrix	brain
5	chr14:39756600-39819600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr14:39756800-39797800	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr14:39757400-39796000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr14:39757400-39843800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr14:39759400-39801800	Weak transcription	NHLF	lung
10	chr14:39762400-39801600	Weak transcription	Fetal Brain Male	brain
11	chr14:39764600-39808200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr14:39764600-39818400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr14:39764800-39802400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr14:39764800-39805200	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr14:39765600-39803800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr14:39765600-39807800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr14:39767000-39796000	Weak transcription	Thymus	Thymus
18	chr14:39767200-39801400	Weak transcription	Brain Hippocampus Middle	brain
19	chr14:39767200-39801600	Weak transcription	Right Ventricle	heart
20	chr14:39767200-39833800	Weak transcription	Small Intestine	intestine
21	chr14:39769800-39796000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr14:39769800-39796000	Weak transcription	Dnd41	blood
23	chr14:39769800-39808000	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr14:39770000-39816400	Weak transcription	Colon Smooth Muscle	Colon
25	chr14:39770600-39819800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr14:39770800-39872400	Weak transcription	Colonic Mucosa	Colon
27	chr14:39771800-39796200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr14:39772000-39796200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr14:39772600-39808000	Weak transcription	Fetal Heart	heart
30	chr14:39773200-39802400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr14:39773400-39801800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr14:39778800-39796200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr14:39779000-39801400	Weak transcription	Fetal Thymus	thymus
34	chr14:39780000-39801000	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr14:39781400-39794400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr14:39782800-39808000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr14:39783200-39794400	Strong transcription	Fetal Intestine Large	intestine
38	chr14:39785000-39794400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr14:39785200-39798200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr14:39785200-39798800	Strong transcription	Duodenum Mucosa	Duodenum
41	chr14:39785600-39802000	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr14:39785800-39796000	Weak transcription	Brain Anterior Caudate	brain
43	chr14:39786400-39801400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr14:39786400-39801600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr14:39786600-39796000	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr14:39786600-39796000	Weak transcription	Brain Substantia Nigra	brain
47	chr14:39786600-39801000	Weak transcription	Ovary	ovary
48	chr14:39786600-39801200	Weak transcription	Rectal Smooth Muscle	rectum
49	chr14:39786600-39801600	Weak transcription	Aorta	Aorta
50	chr14:39786600-39801600	Weak transcription	Esophagus	oesophagus

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