Variant report

Variant	rs2291474
Chromosome Location	chr4:48427260-48427261
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48426298..48428029-chr4:48428848..48431056,2	MCF-7	breast:

Extended variants
information (count: 95 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10003230	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10026398	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10029785	0.83[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs10805168	0.84[ASN][1000 genomes]
rs10938534	0.81[JPT][hapmap]
rs1117010	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11731383	0.81[ASN][1000 genomes]
rs11945562	0.86[JPT][hapmap]
rs12503644	0.94[ASN][1000 genomes]
rs12507206	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12511991	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12645951	0.87[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12649527	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12649528	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13105385	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13115295	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13133788	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13148849	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13150017	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1352433	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1352434	0.84[ASN][1000 genomes]
rs1472967	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs1488647	0.81[ASN][1000 genomes]
rs1507865	0.81[JPT][hapmap]
rs1586540	0.87[ASN][1000 genomes]
rs1703973	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1876469	0.81[JPT][hapmap]
rs1948167	0.87[ASN][1000 genomes]
rs2029348	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2291475	0.88[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2353312	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2353314	0.84[ASN][1000 genomes]
rs2353315	0.91[ASN][1000 genomes]
rs2353855	0.81[ASN][1000 genomes]
rs28409655	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28470767	0.81[JPT][hapmap]
rs34975258	0.91[ASN][1000 genomes]
rs35758434	0.87[ASN][1000 genomes]
rs368609	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs372825	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3828496	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs392187	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs403495	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs404348	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs404445	0.83[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs404656	0.80[ASN][1000 genomes]
rs411261	0.82[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs421336	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs421833	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs429969	0.80[ASN][1000 genomes]
rs432927	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs445892	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs449376	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs450498	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4536901	0.81[JPT][hapmap]
rs4694895	0.87[ASN][1000 genomes]
rs4695377	0.81[ASN][1000 genomes]
rs4695391	0.81[JPT][hapmap]
rs62309425	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62309455	0.80[ASN][1000 genomes]
rs62309458	0.81[ASN][1000 genomes]
rs6447634	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6447635	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6816010	0.87[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6816352	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6821277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6829705	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6829716	0.86[JPT][hapmap]
rs6834339	0.81[ASN][1000 genomes]
rs6836010	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6836632	0.86[JPT][hapmap]
rs6837335	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6838613	0.82[ASN][1000 genomes]
rs6843340	0.81[JPT][hapmap]
rs6844211	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6848073	0.88[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6848395	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7438704	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7654770	0.86[JPT][hapmap]
rs7668529	0.81[EUR][1000 genomes]
rs7672892	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7674269	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7678164	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7678379	0.86[JPT][hapmap]
rs7697851	0.86[JPT][hapmap]
rs923372	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs923373	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9291323	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs937888	0.81[JPT][hapmap]
rs974014	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs974015	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs974016	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs992423	0.86[JPT][hapmap]
rs9996532	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3435642	chr4:48427217-48427769	Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2291474	SLAIN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48382200-48431800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr4:48387600-48431400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr4:48391600-48434000	Weak transcription	Fetal Heart	heart
4	chr4:48400000-48431000	Weak transcription	Brain Angular Gyrus	brain
5	chr4:48406200-48433200	Weak transcription	NHEK	skin
6	chr4:48413200-48430000	Weak transcription	Aorta	Aorta
7	chr4:48413200-48431800	Weak transcription	Brain Substantia Nigra	brain
8	chr4:48413400-48431600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr4:48420800-48427600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr4:48421000-48428400	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr4:48421800-48428000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr4:48421800-48429400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr4:48422600-48431600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr4:48422600-48432000	Weak transcription	Psoas Muscle	Psoas
15	chr4:48422600-48433200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr4:48422600-48433600	Weak transcription	Esophagus	oesophagus
17	chr4:48422600-48434400	Weak transcription	Brain Germinal Matrix	brain
18	chr4:48423200-48433200	Weak transcription	Gastric	stomach
19	chr4:48423400-48438200	Weak transcription	Fetal Intestine Small	intestine
20	chr4:48423600-48428000	Strong transcription	HSMM	muscle
21	chr4:48423600-48433200	Weak transcription	Pancreas	Pancrea
22	chr4:48424400-48430200	Weak transcription	Fetal Stomach	stomach
23	chr4:48424400-48432200	Weak transcription	Brain Hippocampus Middle	brain
24	chr4:48424400-48432400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr4:48424600-48432000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr4:48424800-48430400	Weak transcription	Colonic Mucosa	Colon
27	chr4:48425000-48429000	Weak transcription	Fetal Muscle Trunk	muscle
28	chr4:48425000-48431000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr4:48425000-48431600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:48425000-48431800	Weak transcription	GM12878-XiMat	blood
31	chr4:48425000-48433200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr4:48425200-48427400	Weak transcription	Rectal Smooth Muscle	rectum
33	chr4:48425200-48427600	Weak transcription	Right Ventricle	heart
34	chr4:48425200-48429200	Weak transcription	Fetal Brain Female	brain
35	chr4:48425200-48429200	Weak transcription	Fetal Muscle Leg	muscle
36	chr4:48425200-48430000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr4:48425200-48431000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr4:48425200-48432000	Weak transcription	Brain Cingulate Gyrus	brain
39	chr4:48425200-48432600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr4:48425200-48433000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr4:48425200-48433200	Weak transcription	HUVEC	blood vessel
42	chr4:48425200-48433800	Weak transcription	Stomach Mucosa	stomach
43	chr4:48425200-48441600	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr4:48425400-48429000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr4:48425400-48431000	Weak transcription	Fetal Kidney	kidney
46	chr4:48425400-48433200	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr4:48425400-48438400	Weak transcription	HSMMtube	muscle
48	chr4:48425600-48431800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr4:48425600-48432800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr4:48425800-48428600	Weak transcription	Primary T cells fromperipheralblood	blood

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