Variant report

Variant	rs17302367
Chromosome Location	chr1:174988736-174988737
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr1:174988715-174988956	K562	blood:	n/a	n/a
2	NR2F2	chr1:174988533-174988974	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:174966455..174979047-chr1:174985921..174994239,29	MCF-7	breast:

Variant related genes	Relation type
MRPS14	TF binding region
ENSG00000116161	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1012182	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1034462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1058741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798324	0.81[ASN][1000 genomes]
rs10798327	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs10912843	0.86[JPT][hapmap]
rs10912853	0.86[JPT][hapmap]
rs10912857	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10912871	0.83[EUR][1000 genomes]
rs11800350	0.81[ASN][1000 genomes]
rs11809803	0.81[ASN][1000 genomes]
rs11810508	0.81[ASN][1000 genomes]
rs12063093	0.81[ASN][1000 genomes]
rs12078839	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs12094876	0.86[JPT][hapmap]
rs1231826	0.81[ASN][1000 genomes]
rs1231827	0.81[ASN][1000 genomes]
rs1231829	0.86[JPT][hapmap]
rs1329281	0.81[ASN][1000 genomes]
rs1613634	0.81[ASN][1000 genomes]
rs1618207	0.81[ASN][1000 genomes]
rs1622802	0.81[ASN][1000 genomes]
rs1653630	0.81[ASN][1000 genomes]
rs1653634	0.81[ASN][1000 genomes]
rs16847624	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs17302033	0.86[JPT][hapmap];0.92[YRI][hapmap]
rs17302165	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1754352	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1754353	0.81[ASN][1000 genomes]
rs1793292	0.81[ASN][1000 genomes]
rs1793294	0.81[ASN][1000 genomes]
rs1793298	0.81[ASN][1000 genomes]
rs1793305	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1793316	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1793318	0.81[ASN][1000 genomes]
rs1883139	0.81[ASN][1000 genomes]
rs1894199	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1894201	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1894680	0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2003378	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2157541	0.86[JPT][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2157567	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2183202	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2981893	0.81[ASN][1000 genomes]
rs2981896	0.81[ASN][1000 genomes]
rs2987872	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2987873	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2987875	0.81[ASN][1000 genomes]
rs2987876	0.81[ASN][1000 genomes]
rs3118982	0.81[ASN][1000 genomes]
rs3118986	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs3118987	0.86[JPT][hapmap]
rs34390425	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3766697	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4651205	0.86[JPT][hapmap]
rs4651231	0.86[JPT][hapmap]
rs4651235	0.81[ASN][1000 genomes]
rs4652797	0.81[ASN][1000 genomes]
rs55722026	0.85[ASN][1000 genomes]
rs55774740	0.88[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55844798	0.81[ASN][1000 genomes]
rs60811893	0.81[ASN][1000 genomes]
rs6425298	0.81[ASN][1000 genomes]
rs6425300	0.81[ASN][1000 genomes]
rs6425301	0.81[ASN][1000 genomes]
rs6425302	0.86[JPT][hapmap]
rs6670315	0.86[JPT][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6684515	0.86[JPT][hapmap]
rs6686872	0.81[ASN][1000 genomes]
rs6687616	0.81[ASN][1000 genomes]
rs6690754	0.81[ASN][1000 genomes]
rs6693979	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs6696465	0.81[ASN][1000 genomes]
rs6697561	0.86[JPT][hapmap]
rs67054007	0.82[ASN][1000 genomes]
rs72715300	0.81[ASN][1000 genomes]
rs72717608	0.81[ASN][1000 genomes]
rs72717616	0.81[ASN][1000 genomes]
rs72717630	0.81[ASN][1000 genomes]
rs72717650	0.81[ASN][1000 genomes]
rs72717670	0.82[ASN][1000 genomes]
rs74128535	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7516410	0.86[JPT][hapmap]
rs7521109	0.81[ASN][1000 genomes]
rs7531032	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7543147	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs7547658	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs7554767	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs913686	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs913688	0.81[ASN][1000 genomes]
rs9425787	0.81[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	nsv947512	chr1:174984818-175000909	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17302367	RABGAP1L	cis	Esophagus Muscularis	GTEx
rs17302367	RP11-160H22.5	cis	Thyroid	GTEx
rs17302367	MRPS14	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174970000-174991800	Weak transcription	Stomach Mucosa	stomach
2	chr1:174971000-174991600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:174973000-174990600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:174973600-174990400	Strong transcription	Primary T cells from cord blood	blood
5	chr1:174973800-174988800	Strong transcription	Primary B cells from peripheral blood	blood
6	chr1:174973800-174988800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr1:174973800-174989800	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr1:174974200-174988800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:174974200-174990200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr1:174974800-174989400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr1:174977400-174991800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:174977800-174991800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr1:174978200-174991400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr1:174983000-174991000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr1:174983000-174991600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr1:174983600-174991400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr1:174985600-174989400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:174986200-174991400	Weak transcription	Psoas Muscle	Psoas
19	chr1:174987000-174990200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr1:174987000-174991600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:174987000-174991600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr1:174987000-174991600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:174987000-174991600	Weak transcription	HSMM	muscle
24	chr1:174987000-174991800	Weak transcription	Esophagus	oesophagus
25	chr1:174987200-174990400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:174987200-174991400	Weak transcription	Brain Substantia Nigra	brain
27	chr1:174987200-174991600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr1:174987200-174991800	Weak transcription	Aorta	Aorta
29	chr1:174987200-174991800	Weak transcription	Ovary	ovary
30	chr1:174987200-174991800	Weak transcription	Pancreas	Pancrea
31	chr1:174987200-174992000	Weak transcription	Small Intestine	intestine
32	chr1:174987400-174991600	Weak transcription	Fetal Intestine Small	intestine
33	chr1:174987600-174990000	Weak transcription	NHEK	skin
34	chr1:174987600-174990200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:174987600-174990800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr1:174987600-174991000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr1:174987600-174991200	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr1:174987600-174991400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr1:174987600-174991600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr1:174987600-174991600	Weak transcription	Brain Hippocampus Middle	brain
41	chr1:174987600-174991600	Weak transcription	Fetal Lung	lung
42	chr1:174987600-174991600	Weak transcription	Rectal Smooth Muscle	rectum
43	chr1:174987600-174991600	Weak transcription	NH-A	brain
44	chr1:174987600-174991800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr1:174987600-174991800	Weak transcription	Brain Germinal Matrix	brain
46	chr1:174987800-174989600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr1:174987800-174990000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr1:174987800-174990000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr1:174987800-174990000	Weak transcription	Fetal Intestine Large	intestine
50	chr1:174987800-174990000	Weak transcription	HepG2	liver

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