Variant report

Variant	rs3175
Chromosome Location	chr2:153618773-153618774
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:153573784..153577602-chr2:153618161..153622533,3	K562	blood:
2	chr2:153559758..153562464-chr2:153616501..153619452,2	K562	blood:
3	chr2:153618496..153621083-chr2:153625320..153627724,2	K562	blood:
4	chr2:153600659..153603319-chr2:153618153..153620356,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177917	Chromatin interaction
ENSG00000196504	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10172024	0.84[JPT][hapmap]
rs1036526	0.84[JPT][hapmap]
rs1065266	0.88[CHD][hapmap];0.84[JPT][hapmap]
rs10931229	0.84[JPT][hapmap]
rs1128804	0.88[CHD][hapmap];0.84[JPT][hapmap]
rs11899051	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs12477881	0.83[JPT][hapmap]
rs12621561	1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs13010731	0.84[JPT][hapmap]
rs13031469	0.83[JPT][hapmap]
rs13419068	1.00[JPT][hapmap]
rs1370498	0.88[CHD][hapmap];0.84[JPT][hapmap]
rs1437678	0.84[JPT][hapmap]
rs16831548	0.88[CHD][hapmap];0.84[JPT][hapmap]
rs16831740	0.91[CHD][hapmap];0.84[JPT][hapmap]
rs17328734	0.88[CHD][hapmap]
rs17400645	0.80[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap]
rs1962313	0.81[CEU][hapmap];0.80[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs1986743	0.81[CEU][hapmap];0.80[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1992146	0.84[JPT][hapmap]
rs2118377	0.88[CHD][hapmap];0.84[JPT][hapmap]
rs2346539	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs2346542	0.84[JPT][hapmap]
rs2346543	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs2346549	0.80[CEU][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs2346550	0.88[CHD][hapmap];0.84[JPT][hapmap]
rs3171980	0.88[CHD][hapmap];0.84[JPT][hapmap]
rs3748937	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3748938	0.81[CEU][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3748939	0.84[JPT][hapmap]
rs3762503	0.94[CHD][hapmap];0.95[JPT][hapmap]
rs3762507	0.88[CHD][hapmap];0.84[JPT][hapmap]
rs4233660	0.81[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4267470	0.81[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs4664121	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs4664122	0.84[JPT][hapmap]
rs4664601	0.94[CHD][hapmap];0.95[JPT][hapmap]
rs4664604	0.84[JPT][hapmap]
rs4664605	0.80[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs4664606	0.80[CEU][hapmap];0.80[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4664607	0.84[JPT][hapmap]
rs4664610	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs61049574	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6434128	0.89[CHD][hapmap]
rs6434161	0.84[JPT][hapmap]
rs6434162	0.84[JPT][hapmap]
rs6723574	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6744923	0.85[JPT][hapmap]
rs6748160	1.00[JPT][hapmap]
rs7556673	0.81[CEU][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap]
rs7558920	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7560393	0.84[JPT][hapmap]
rs7576847	0.94[JPT][hapmap]
rs7582253	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs7589899	0.91[CHD][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7593347	0.83[JPT][hapmap]
rs7599946	0.81[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs7608603	0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9288121	0.84[JPT][hapmap]
rs9288125	0.88[CHD][hapmap];0.84[JPT][hapmap]
rs9789521	0.91[CHD][hapmap];0.95[JPT][hapmap]

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	nsv834421	chr2:153470109-153664235	Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv3693438	chr2:153505376-153718246	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv834422	chr2:153589448-153743069	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv875294	chr2:153607506-153733325	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3175	ARL6IP6	Cis_1M	lymphoblastoid	RTeQTL
rs3175	LYPD6	cis	parietal	SCAN
rs3175	ARL6IP6	cis	cerebellum	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153575800-153621400	Weak transcription	Pancreas	Pancrea
2	chr2:153587600-153621600	Weak transcription	NHEK	skin
3	chr2:153588600-153619400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:153590400-153620400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:153592200-153618800	Weak transcription	HSMMtube	muscle
6	chr2:153593200-153618800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr2:153593200-153628400	Weak transcription	Fetal Kidney	kidney
8	chr2:153593600-153621800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr2:153593800-153620000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr2:153593800-153621400	Weak transcription	HMEC	breast
11	chr2:153593800-153621600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr2:153595200-153621800	Weak transcription	Aorta	Aorta
13	chr2:153595200-153622000	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr2:153595400-153621600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:153596400-153619400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr2:153596600-153621400	Weak transcription	Ovary	ovary
17	chr2:153596600-153621400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr2:153597000-153619800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr2:153597600-153620600	Strong transcription	Dnd41	blood
20	chr2:153600600-153623400	Weak transcription	Colon Smooth Muscle	Colon
21	chr2:153601400-153619600	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr2:153602200-153620600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr2:153602200-153621200	Weak transcription	Fetal Brain Female	brain
24	chr2:153602400-153620600	Weak transcription	Fetal Brain Male	brain
25	chr2:153606600-153619400	Weak transcription	Fetal Heart	heart
26	chr2:153607600-153619400	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr2:153608800-153620600	Strong transcription	Primary B cells from cord blood	blood
28	chr2:153608800-153621200	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr2:153609400-153621400	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr2:153609400-153621800	Weak transcription	Spleen	Spleen
31	chr2:153609600-153619200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr2:153609600-153619800	Weak transcription	Fetal Intestine Large	intestine
33	chr2:153611600-153619800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr2:153611800-153619400	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr2:153611800-153620200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr2:153612000-153619000	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr2:153612200-153619800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr2:153612200-153620000	Weak transcription	Lung	lung
39	chr2:153612200-153620200	Weak transcription	Brain Germinal Matrix	brain
40	chr2:153612200-153621800	Weak transcription	Esophagus	oesophagus
41	chr2:153612400-153621000	Weak transcription	Fetal Intestine Small	intestine
42	chr2:153612400-153621800	Weak transcription	Fetal Stomach	stomach
43	chr2:153612600-153619200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr2:153612800-153619200	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr2:153612800-153620400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr2:153613200-153619600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr2:153613400-153619000	Strong transcription	HSMM	muscle
48	chr2:153613400-153620600	Strong transcription	Duodenum Mucosa	Duodenum
49	chr2:153613800-153621400	Weak transcription	GM12878-XiMat	blood
50	chr2:153613800-153622600	Weak transcription	A549	lung

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