Variant report

Variant	rs2037594
Chromosome Location	chr1:85871618-85871619
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1001604	0.91[YRI][hapmap];0.90[AFR][1000 genomes]
rs1006988	0.94[CEU][hapmap];0.83[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs1006989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10489510	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs10489513	0.82[LWK][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs10747318	0.83[CEU][hapmap];0.89[EUR][1000 genomes]
rs10782549	0.83[CEU][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes]
rs10873701	0.83[CEU][hapmap];0.89[EUR][1000 genomes]
rs10873702	0.86[LWK][hapmap]
rs1146383	0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12029221	0.87[EUR][1000 genomes]
rs12033483	0.98[GIH][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes]
rs12034249	0.83[CEU][hapmap];0.89[EUR][1000 genomes]
rs12035116	0.83[EUR][1000 genomes]
rs12038426	0.83[EUR][1000 genomes]
rs12042780	0.81[EUR][1000 genomes]
rs12044537	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs12047189	0.81[EUR][1000 genomes]
rs12140103	0.86[AFR][1000 genomes]
rs1261681	0.85[EUR][1000 genomes]
rs1342323	0.83[CEU][hapmap];0.98[GIH][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes]
rs1357635	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs1357636	0.83[CEU][hapmap];0.98[GIH][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes]
rs1391556	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs1523995	0.83[CEU][hapmap];0.90[EUR][1000 genomes]
rs1554597	0.83[LWK][hapmap]
rs1608537	0.89[EUR][1000 genomes]
rs17384213	0.83[CEU][hapmap];0.89[EUR][1000 genomes]
rs17388696	0.95[GIH][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs1884139	0.80[AFR][1000 genomes]
rs1965876	0.89[EUR][1000 genomes]
rs2012683	0.85[AFR][1000 genomes]
rs2016104	0.83[CEU][hapmap];0.89[EUR][1000 genomes]
rs2064510	0.85[EUR][1000 genomes]
rs2124139	0.83[CEU][hapmap];0.98[GIH][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes]
rs2300633	0.83[CEU][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs233053	0.84[LWK][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs2389948	0.89[EUR][1000 genomes]
rs2892888	0.83[AFR][1000 genomes]
rs3851268	0.87[EUR][1000 genomes]
rs4428939	0.89[EUR][1000 genomes]
rs4512701	0.85[EUR][1000 genomes]
rs4631749	0.85[EUR][1000 genomes]
rs4949889	0.82[EUR][1000 genomes]
rs4949897	0.82[EUR][1000 genomes]
rs4949898	0.83[EUR][1000 genomes]
rs4949899	0.85[EUR][1000 genomes]
rs4949900	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs499869	0.87[EUR][1000 genomes]
rs539714	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs600098	0.80[EUR][1000 genomes]
rs604974	0.87[EUR][1000 genomes]
rs6420965	0.88[EUR][1000 genomes]
rs6576763	0.82[LWK][hapmap];0.83[MKK][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs6576764	0.80[AFR][1000 genomes]
rs6576765	0.80[LWK][hapmap];0.83[MKK][hapmap];0.81[YRI][hapmap]
rs6576766	0.82[AFR][1000 genomes]
rs659070	0.88[GIH][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap]
rs6672870	0.83[CEU][hapmap];0.98[GIH][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs72722663	0.82[EUR][1000 genomes]
rs72722691	0.83[EUR][1000 genomes]
rs72724608	0.84[EUR][1000 genomes]
rs731194	0.83[EUR][1000 genomes]
rs7515261	0.83[CEU][hapmap];0.89[EUR][1000 genomes]
rs7525786	0.84[AFR][1000 genomes]
rs7539738	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7555670	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs990916	0.83[CEU][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv830470	chr1:85820775-86014080	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1008877	chr1:85843238-85897570	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv3393958	chr1:85857980-85874598	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2037594	BCL10	cis	multi-tissue	Pritchard

Chromatin state (count:50 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85856000-85872800	Weak transcription	Fetal Intestine Small	intestine
2	chr1:85862200-85874600	Weak transcription	Pancreas	Pancrea
3	chr1:85864000-85872600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr1:85864400-85871800	Weak transcription	NH-A	brain
5	chr1:85864400-85872200	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr1:85864400-85873000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr1:85864400-85874600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:85864800-85876800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr1:85865400-85872800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:85868600-85872800	Enhancers	Liver	Liver
11	chr1:85869000-85872800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:85869200-85873200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr1:85869400-85872200	Weak transcription	Fetal Kidney	kidney
14	chr1:85869800-85871800	Enhancers	Colon Smooth Muscle	Colon
15	chr1:85869800-85874400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:85870000-85871800	Enhancers	Ovary	ovary
17	chr1:85870000-85873000	Enhancers	HSMMtube	muscle
18	chr1:85870200-85872600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr1:85870200-85874800	Enhancers	Osteobl	bone
20	chr1:85870400-85872800	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr1:85870400-85872800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr1:85870600-85871800	Enhancers	Fetal Stomach	stomach
23	chr1:85870600-85872800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr1:85870600-85872800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr1:85870800-85871800	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr1:85870800-85872000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:85870800-85872600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:85870800-85872600	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr1:85870800-85872800	Enhancers	NHDF-Ad	bronchial
30	chr1:85871000-85871800	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr1:85871000-85871800	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr1:85871000-85872200	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr1:85871000-85872200	Genic enhancers	HUVEC	blood vessel
34	chr1:85871000-85872800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:85871200-85871800	Genic enhancers	Muscle Satellite Cultured Cells	--
36	chr1:85871200-85871800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:85871400-85871800	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr1:85871400-85871800	Enhancers	A549	lung
39	chr1:85871400-85871800	Enhancers	NHLF	lung
40	chr1:85871400-85872000	Enhancers	Fetal Lung	lung
41	chr1:85871400-85872800	Weak transcription	Brain Substantia Nigra	brain
42	chr1:85871400-85873000	Weak transcription	Brain Anterior Caudate	brain
43	chr1:85871400-85874000	Enhancers	HSMM	muscle
44	chr1:85871400-85878400	Weak transcription	Fetal Muscle Leg	muscle
45	chr1:85871600-85872200	Enhancers	Adipose Nuclei	Adipose
46	chr1:85871600-85872200	Enhancers	Rectal Smooth Muscle	rectum
47	chr1:85871600-85872600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr1:85871600-85872800	Weak transcription	Aorta	Aorta
49	chr1:85871600-85873200	Weak transcription	Stomach Mucosa	stomach
50	chr1:85871600-85876600	Weak transcription	HUES6 Cell Line	embryonic stem cell

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