Variant report

Variant	rs13123498
Chromosome Location	chr4:144316247-144316248
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:144315927..144318308-chr4:144352192..144353716,2	K562	blood:
2	chr4:144279896..144282516-chr4:144316177..144318703,2	K562	blood:
3	chr4:144316084..144318311-chr4:144327317..144330224,3	K562	blood:
4	chr4:144105239..144107122-chr4:144315713..144318669,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SMARCA5-7	chr4:144315970-144316873	NONHSAT098555

Variant related genes	Relation type
ENSG00000250326	Chromatin interaction
ENSG00000170185	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10013047	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1027851	0.91[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1027852	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10519691	0.82[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap]
rs11100786	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11100787	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11100788	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11100789	0.87[ASN][1000 genomes]
rs11730569	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11945731	0.93[ASN][1000 genomes]
rs12647531	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12649592	0.96[ASN][1000 genomes]
rs13101346	0.94[ASN][1000 genomes]
rs1397526	0.89[ASN][1000 genomes]
rs1397528	1.00[CHB][hapmap];0.90[CHD][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1472873	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1510879	0.93[ASN][1000 genomes]
rs1510880	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.96[ASN][1000 genomes]
rs17017757	0.81[ASW][hapmap]
rs1866756	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2048408	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2055730	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2119270	0.96[ASN][1000 genomes]
rs2196908	0.94[ASN][1000 genomes]
rs2196909	0.86[CEU][hapmap];0.94[ASN][1000 genomes]
rs300890	0.84[JPT][hapmap]
rs300893	0.84[JPT][hapmap]
rs300894	0.84[JPT][hapmap]
rs300895	0.84[JPT][hapmap]
rs300904	0.84[JPT][hapmap]
rs300905	0.84[JPT][hapmap]
rs300910	0.85[ASN][1000 genomes]
rs300911	0.89[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs300912	0.89[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs300913	0.89[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs300914	0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs300915	0.89[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs300916	0.89[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs300917	0.89[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs300918	0.81[ASN][1000 genomes]
rs300919	0.84[JPT][hapmap]
rs34095331	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs34439737	0.94[ASN][1000 genomes]
rs3792652	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3792653	0.83[CEU][hapmap];0.96[ASN][1000 genomes]
rs3792655	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3805238	1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs3805245	0.96[ASN][1000 genomes]
rs3805246	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3805247	0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3805249	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3805251	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.96[ASN][1000 genomes]
rs3805252	0.96[ASN][1000 genomes]
rs3805253	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.96[ASN][1000 genomes]
rs3805254	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3805256	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[ASN][1000 genomes]
rs3805257	0.89[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3828512	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3828513	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3828514	0.96[ASN][1000 genomes]
rs55758499	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55894236	0.97[ASN][1000 genomes]
rs6537154	0.95[ASN][1000 genomes]
rs6537155	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.96[ASN][1000 genomes]
rs713140	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs719392	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7680959	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs906571	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13123498	ABCE1	cis	parietal	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:144303000-144318000	Weak transcription	HSMM	muscle
2	chr4:144303200-144317800	Weak transcription	Gastric	stomach
3	chr4:144303400-144326600	Weak transcription	Colonic Mucosa	Colon
4	chr4:144304200-144320000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr4:144304600-144317000	Weak transcription	K562	blood
6	chr4:144306600-144318000	Weak transcription	Aorta	Aorta
7	chr4:144307400-144323600	Enhancers	Brain Hippocampus Middle	brain
8	chr4:144308000-144316400	Enhancers	Brain Substantia Nigra	brain
9	chr4:144308800-144319400	Enhancers	Brain Cingulate Gyrus	brain
10	chr4:144309200-144317000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:144309200-144327600	Weak transcription	Esophagus	oesophagus
12	chr4:144310200-144317000	Weak transcription	Left Ventricle	heart
13	chr4:144310200-144325600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr4:144310800-144317600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr4:144311200-144320400	Weak transcription	Stomach Mucosa	stomach
16	chr4:144311400-144320000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr4:144311600-144321600	Enhancers	Brain Angular Gyrus	brain
18	chr4:144312200-144317000	Weak transcription	Right Atrium	heart
19	chr4:144312200-144317000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr4:144312200-144317200	Weak transcription	Pancreas	Pancrea
21	chr4:144312200-144321000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr4:144312400-144319000	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr4:144312400-144323600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr4:144312600-144323800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr4:144312600-144326400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr4:144312600-144328600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr4:144312800-144317000	Weak transcription	Fetal Intestine Large	intestine
28	chr4:144312800-144317600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr4:144312800-144317600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr4:144312800-144324000	Weak transcription	Fetal Intestine Small	intestine
31	chr4:144312800-144331400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr4:144312800-144336800	Weak transcription	Fetal Muscle Trunk	muscle
33	chr4:144313000-144319200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr4:144313000-144320200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr4:144313000-144323800	Weak transcription	Fetal Muscle Leg	muscle
36	chr4:144313200-144318000	Weak transcription	NH-A	brain
37	chr4:144313200-144319000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr4:144313200-144319200	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr4:144313200-144320400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr4:144313400-144320400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr4:144313400-144323000	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr4:144313400-144323400	Weak transcription	Fetal Brain Female	brain
43	chr4:144313400-144323600	Weak transcription	Primary hematopoietic stem cells	blood
44	chr4:144313400-144324000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr4:144313600-144317600	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr4:144313600-144319600	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr4:144313800-144317000	Weak transcription	Fetal Stomach	stomach
48	chr4:144313800-144317600	Weak transcription	Osteobl	bone
49	chr4:144313800-144318400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr4:144313800-144320400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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