Variant report

Variant	rs2171958
Chromosome Location	chr1:179176398-179176399
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179174832..179177556-chr1:179180211..179184356,3	MCF-7	breast:
2	chr1:179173955..179176845-chr1:179197324..179198922,2	MCF-7	breast:
3	chr1:179176232..179178447-chr1:179186327..179188958,2	K562	blood:
4	chr1:179169821..179172184-chr1:179175526..179179227,3	K562	blood:
5	chr1:179168253..179170911-chr1:179175778..179178342,2	K562	blood:

Variant related genes	Relation type
ENSG00000231564	Chromatin interaction
ENSG00000201619	Chromatin interaction
ENSG00000143322	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs1078872	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs10913690	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs10913692	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.87[TSI][hapmap];0.92[YRI][hapmap];0.84[EUR][1000 genomes]
rs10913693	0.85[EUR][1000 genomes]
rs10913697	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs12130276	0.86[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap]
rs12132572	0.86[ASN][1000 genomes]
rs1325195	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1763022	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1807916	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1826183	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1856968	0.82[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap]
rs2050923	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2066279	0.95[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs2087559	0.81[ASN][1000 genomes]
rs2130576	0.91[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs2171959	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs2306941	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2486998	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2487563	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2493123	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2493124	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs2636265	0.90[ASN][1000 genomes]
rs2636272	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2636274	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs2636275	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2636276	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs2636277	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2636278	0.85[GIH][hapmap]
rs2636280	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs2636282	0.92[ASN][1000 genomes]
rs2636291	0.86[EUR][1000 genomes]
rs2636293	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap]
rs2791936	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2791940	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs2791941	0.90[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs2791944	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2791945	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2793790	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2793793	0.81[ASN][1000 genomes]
rs2793794	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2793796	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs2793797	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs2793798	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs2793800	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2793801	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2793802	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2793803	0.95[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs2793810	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2793812	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs2793813	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2793816	0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs2816166	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2816168	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[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];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2816183	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2816184	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2816186	0.95[CHB][hapmap]
rs2816187	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2816189	0.81[ASN][1000 genomes]
rs2816190	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap]
rs2816191	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2816193	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap]
rs2816197	0.88[ASN][1000 genomes]
rs2816198	0.95[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs2816199	0.95[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs2816200	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2816201	1.00[CHB][hapmap];0.86[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2816202	0.88[ASN][1000 genomes]
rs2816203	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs2816204	0.88[ASN][1000 genomes]
rs2816207	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2816208	0.92[ASN][1000 genomes]
rs2816211	0.90[ASN][1000 genomes]
rs2816212	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2816213	0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs2816214	0.91[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs2816218	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3121198	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3122376	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs377785	0.88[ASN][1000 genomes]
rs3813642	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs3813643	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs3829794	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.92[YRI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs411266	0.95[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs413613	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs434283	0.88[ASN][1000 genomes]
rs451088	0.95[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs4651013	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs915337	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs9286921	0.87[EUR][1000 genomes]
rs9425839	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs965401	0.81[ASN][1000 genomes]
rs9662858	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[EUR][1000 genomes]
rs9726961	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs9728480	0.95[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap]
rs9729129	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2171958	FAM20B	cis	parietal	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179117800-179186000	Weak transcription	Fetal Stomach	stomach
2	chr1:179122000-179189400	Weak transcription	Primary B cells from cord blood	blood
3	chr1:179139400-179196800	Weak transcription	Pancreas	Pancrea
4	chr1:179148000-179186000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:179148400-179185800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:179150800-179178000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:179150800-179180400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr1:179156400-179177800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:179157400-179197400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:179157400-179197600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:179157600-179177800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:179160200-179186800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr1:179160800-179188000	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr1:179162800-179177800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:179167800-179177800	Weak transcription	Fetal Heart	heart
16	chr1:179169000-179197400	Weak transcription	NHEK	skin
17	chr1:179169600-179181200	Weak transcription	GM12878-XiMat	blood
18	chr1:179170200-179184000	Weak transcription	Fetal Intestine Small	intestine
19	chr1:179170200-179197200	Weak transcription	Fetal Intestine Large	intestine
20	chr1:179171800-179186600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:179172200-179186600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr1:179172800-179189800	Weak transcription	Primary T cells from cord blood	blood
23	chr1:179173000-179187600	Weak transcription	Small Intestine	intestine
24	chr1:179174600-179176400	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr1:179174800-179177400	Weak transcription	Aorta	Aorta
26	chr1:179174800-179177600	Weak transcription	Gastric	stomach
27	chr1:179174800-179177600	Weak transcription	K562	blood
28	chr1:179174800-179184000	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr1:179174800-179186600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:179175000-179176400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:179175200-179177800	Enhancers	Pancreatic Islets	Pancreatic Islet
32	chr1:179175200-179189200	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr1:179175600-179176400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:179175600-179176400	Flanking Active TSS	Fetal Brain Male	brain
35	chr1:179175600-179176600	Enhancers	Brain Substantia Nigra	brain
36	chr1:179175600-179177000	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr1:179175800-179176400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr1:179175800-179176400	Flanking Active TSS	Brain Anterior Caudate	brain
39	chr1:179175800-179176400	Enhancers	Fetal Lung	lung
40	chr1:179176000-179176400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr1:179176000-179176400	Flanking Active TSS	Brain Angular Gyrus	brain
42	chr1:179176000-179176400	Flanking Active TSS	Brain Germinal Matrix	brain
43	chr1:179176000-179176400	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr1:179176000-179176400	Enhancers	Left Ventricle	heart
45	chr1:179176000-179176400	Flanking Active TSS	Ovary	ovary
46	chr1:179176000-179176400	Enhancers	Psoas Muscle	Psoas
47	chr1:179176000-179176400	Enhancers	HSMM	muscle
48	chr1:179176000-179176400	Active TSS	NHLF	lung
49	chr1:179176000-179176600	Flanking Active TSS	Fetal Brain Female	brain
50	chr1:179176000-179179400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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