Variant report

Variant	rs17302165
Chromosome Location	chr1:174939375-174939376
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:174937958..174940794-chr1:174967575..174969945,2	MCF-7	breast:
2	chr1:174937198..174939859-chr1:174967245..174970067,3	MCF-7	breast:
3	chr1:174932632..174935531-chr1:174937722..174939666,3	MCF-7	breast:
4	chr1:174938092..174940324-chr1:174940877..174942790,2	MCF-7	breast:
5	chr1:174939098..174941697-chr1:174958676..174960962,2	K562	blood:
6	chr1:174927580..174945830-chr1:174955726..174971213,32	K562	blood:

Variant related genes	Relation type
ENSG00000252552	Chromatin interaction
ENSG00000152061	Chromatin interaction
ENSG00000116161	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1012182	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1034462	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1058741	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10798324	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs10798327	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs10912843	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs10912853	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs10912857	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10912871	0.81[EUR][1000 genomes]
rs12078839	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs12094876	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1231829	0.86[JPT][hapmap]
rs1613634	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1618408	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs1653630	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs16847624	1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs17302033	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs17302367	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	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1754354	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1754360	0.86[JPT][hapmap]
rs1793292	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1793294	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1793298	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1793305	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1793310	0.86[JPT][hapmap]
rs1793316	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1793320	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1894199	0.86[JPT][hapmap]
rs1894201	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1894680	1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2003378	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2157541	1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2157567	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2183202	0.86[JPT][hapmap]
rs2860725	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2987872	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2987873	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs3118986	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs3118987	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs3118988	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs3118990	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs34390425	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3766697	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4651205	0.86[JPT][hapmap]
rs4651231	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs4652797	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs55722026	0.81[ASN][1000 genomes]
rs55774740	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6425298	1.00[CHB][hapmap]
rs6425302	0.86[JPT][hapmap]
rs6670315	1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6684515	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs6687616	1.00[CHB][hapmap]
rs6693979	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs6697561	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs67054007	0.82[ASN][1000 genomes]
rs72717670	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs74128535	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7516410	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs7531032	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7543147	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs7547658	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs7554767	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs913686	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs913687	0.86[JPT][hapmap]

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	esv2755184	chr1:174388343-174970343	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17302165	RP11-160H22.5	cis	Thyroid	GTEx
rs17302165	RABGAP1L	cis	Esophagus Muscularis	GTEx
rs17302165	MRPS14	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174910800-174957000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:174924200-174967800	Weak transcription	Brain Germinal Matrix	brain
3	chr1:174924400-174958200	Weak transcription	Fetal Brain Male	brain
4	chr1:174925000-174940800	Weak transcription	Gastric	stomach
5	chr1:174932600-174941600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:174933000-174953600	Weak transcription	Fetal Heart	heart
7	chr1:174934600-174943800	Weak transcription	Pancreas	Pancrea
8	chr1:174934800-174940400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr1:174934800-174943800	Weak transcription	Aorta	Aorta
10	chr1:174935000-174942200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:174935000-174943800	Weak transcription	Lung	lung
12	chr1:174935000-174959000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr1:174935000-174964000	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr1:174935000-174967000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:174935200-174943400	Weak transcription	Brain Angular Gyrus	brain
16	chr1:174935200-174943400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:174935200-174943800	Weak transcription	Fetal Muscle Leg	muscle
18	chr1:174935200-174959000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr1:174935200-174959600	Weak transcription	Esophagus	oesophagus
20	chr1:174935400-174943600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:174935400-174958400	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr1:174935600-174943800	Weak transcription	Brain Hippocampus Middle	brain
23	chr1:174935800-174959600	Weak transcription	Fetal Kidney	kidney
24	chr1:174936000-174940600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr1:174936000-174943800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr1:174936000-174944600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:174936000-174945000	Weak transcription	NHEK	skin
28	chr1:174936000-174946200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr1:174936000-174950600	Weak transcription	Fetal Brain Female	brain
30	chr1:174936000-174958600	Weak transcription	Brain Substantia Nigra	brain
31	chr1:174936400-174939600	Enhancers	HSMMtube	muscle
32	chr1:174936600-174943400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr1:174936600-174945400	Weak transcription	Fetal Lung	lung
34	chr1:174937000-174940800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr1:174937000-174943800	Weak transcription	Ovary	ovary
36	chr1:174937000-174963600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr1:174937200-174939400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:174937200-174939600	Enhancers	HSMM	muscle
39	chr1:174937200-174940600	Weak transcription	Stomach Mucosa	stomach
40	chr1:174937200-174955000	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr1:174937400-174939400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr1:174937400-174944200	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr1:174937400-174963600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr1:174937600-174940600	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr1:174937800-174939400	Enhancers	Fetal Thymus	thymus
46	chr1:174937800-174939800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:174937800-174942200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr1:174938000-174939600	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr1:174938000-174939600	Genic enhancers	K562	blood
50	chr1:174938000-174940800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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