Variant report

Variant	rs1401383
Chromosome Location	chr2:86122874-86122875
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:85893452..85895413-chr2:86122846..86125699,2	K562	blood:
2	chr2:86114878..86116961-chr2:86120705..86124277,3	MCF-7	breast:
3	chr2:86119817..86123713-chr2:86130856..86134451,3	K562	blood:

Variant related genes	Relation type
ENSG00000168878	Chromatin interaction
ENSG00000272564	Chromatin interaction
ENSG00000115525	Chromatin interaction
ENSG00000232504	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12478916	0.84[CEU][hapmap]
rs12613609	0.88[CEU][hapmap]
rs12714154	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12994053	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13024999	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13025142	0.88[CEU][hapmap];0.90[GIH][hapmap]
rs13028295	0.81[JPT][hapmap]
rs13422640	0.88[CEU][hapmap];0.82[CHB][hapmap]
rs1401385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1533605	0.88[CEU][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap]
rs2010859	0.93[AFR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2083170	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2176627	0.88[CEU][hapmap]
rs2366947	0.88[CEU][hapmap];0.92[GIH][hapmap];0.91[MEX][hapmap]
rs2366950	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2679722	0.90[MKK][hapmap];0.82[TSI][hapmap]
rs28364795	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4313976	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4331504	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4553826	0.88[CEU][hapmap];0.92[GIH][hapmap];0.87[MEX][hapmap]
rs4832015	0.88[CEU][hapmap];0.92[GIH][hapmap];0.87[MEX][hapmap]
rs4832213	0.88[CEU][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes]
rs4832215	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4832219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4832220	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4832221	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6547637	0.88[CEU][hapmap]
rs6707472	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6721125	0.88[CEU][hapmap];0.92[GIH][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap]
rs6726662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6734488	0.88[CEU][hapmap]
rs6753350	0.88[CEU][hapmap]
rs7565996	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs893445	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1401383	ST3GAL5	cis	cerebellum	SCAN
rs1401383	IMMT	cis	cerebellum	SCAN
rs1401383	KCMF1	cis	cerebellum	SCAN
rs1401383	PTCD3	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86117400-86126400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr2:86118200-86126000	Weak transcription	Primary T cells from cord blood	blood
3	chr2:86118200-86126800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr2:86118400-86126600	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr2:86118400-86127600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr2:86118600-86131000	Weak transcription	Thymus	Thymus
7	chr2:86119800-86132200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr2:86120000-86126600	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr2:86120200-86134200	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr2:86120800-86131400	Weak transcription	Pancreas	Pancrea
11	chr2:86121200-86123800	Weak transcription	Lung	lung
12	chr2:86121200-86126600	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr2:86121400-86124000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr2:86121400-86127000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr2:86121400-86128800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr2:86121400-86132000	Weak transcription	Placenta	Placenta
17	chr2:86121600-86125800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr2:86121600-86126800	Weak transcription	Brain Angular Gyrus	brain
19	chr2:86121600-86129000	Weak transcription	Fetal Muscle Leg	muscle
20	chr2:86121600-86129400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr2:86121600-86131800	Weak transcription	Adipose Nuclei	Adipose
22	chr2:86121800-86123200	Enhancers	Brain Substantia Nigra	brain
23	chr2:86121800-86124000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr2:86121800-86127000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr2:86121800-86128800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr2:86122000-86127000	Weak transcription	Brain Anterior Caudate	brain
27	chr2:86122000-86134400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr2:86122200-86123000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:86122200-86123000	ZNF genes & repeats	Primary B cells from cord blood	blood
30	chr2:86122600-86123000	Enhancers	Brain Cingulate Gyrus	brain
31	chr2:86122600-86123200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr2:86122600-86123200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr2:86122600-86123200	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr2:86122600-86123200	ZNF genes & repeats	A549	lung
35	chr2:86122800-86123200	Genic enhancers	Brain Hippocampus Middle	brain

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