Variant report

Variant	rs2157541
Chromosome Location	chr1:174926123-174926124
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:174925608..174927850-chr1:174931467..174933958,2	K562	blood:
2	chr1:174908320..174910168-chr1:174924231..174926585,2	K562	blood:

Variant related genes	Relation type
ENSG00000152061	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1012182	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs1034462	0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs1058741	0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs10798324	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10798327	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10912843	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10912853	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.84[EUR][1000 genomes]
rs10912854	0.86[CEU][hapmap];0.96[YRI][hapmap]
rs10912855	0.85[EUR][1000 genomes]
rs10912857	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12063093	0.84[EUR][1000 genomes]
rs12078839	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs12094876	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[EUR][1000 genomes]
rs1231829	1.00[JPT][hapmap]
rs1329281	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1613634	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1618408	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1622802	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1653630	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16847624	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17302033	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs17302165	1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17302367	0.86[JPT][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1754352	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1754354	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1754360	1.00[JPT][hapmap]
rs1793292	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1793294	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1793298	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1793305	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1793307	1.00[JPT][hapmap]
rs1793310	1.00[JPT][hapmap]
rs1793316	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1793320	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1894199	1.00[JPT][hapmap]
rs1894201	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1894680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2003378	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2156854	0.88[JPT][hapmap]
rs2157567	0.86[ASN][1000 genomes]
rs2183202	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs2860725	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2987872	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2987873	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3118986	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3118987	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3118988	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3118990	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3766697	0.86[ASN][1000 genomes]
rs4480415	0.88[JPT][hapmap]
rs4651205	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs4651231	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[EUR][1000 genomes]
rs4651235	0.84[EUR][1000 genomes]
rs4652797	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs55774740	0.86[ASN][1000 genomes]
rs55793234	0.80[EUR][1000 genomes]
rs6425298	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs6425302	1.00[JPT][hapmap]
rs6425303	0.81[CEU][hapmap]
rs6425306	0.82[EUR][1000 genomes]
rs6670315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6671196	0.81[EUR][1000 genomes]
rs6671272	0.82[EUR][1000 genomes]
rs6671782	0.85[EUR][1000 genomes]
rs6675528	0.81[CEU][hapmap]
rs66836419	0.82[EUR][1000 genomes]
rs6684229	0.85[EUR][1000 genomes]
rs6684515	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[EUR][1000 genomes]
rs6687616	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs6693979	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6696465	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6697561	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs67054007	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67133776	0.83[EUR][1000 genomes]
rs67203477	0.82[EUR][1000 genomes]
rs67903803	0.82[EUR][1000 genomes]
rs72717649	0.82[EUR][1000 genomes]
rs72717650	0.82[EUR][1000 genomes]
rs72717653	0.82[EUR][1000 genomes]
rs72717661	0.81[EUR][1000 genomes]
rs72717670	0.91[EUR][1000 genomes]
rs74128535	0.86[ASN][1000 genomes]
rs7516410	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs7531032	0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs7543147	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[EUR][1000 genomes]
rs7547658	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7554767	0.86[ASN][1000 genomes]
rs913686	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs913687	1.00[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
rs2157541	RP11-160H22.5	cis	Thyroid	GTEx
rs2157541	RABGAP1L	cis	Esophagus Muscularis	GTEx
rs2157541	MRPS14	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174874200-174938200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:174876800-174933600	Weak transcription	Aorta	Aorta
3	chr1:174908000-174926600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr1:174908000-174932400	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr1:174908600-174927400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr1:174908800-174932200	Weak transcription	Primary T cells from cord blood	blood
7	chr1:174910400-174932400	Weak transcription	HSMMtube	muscle
8	chr1:174910800-174957000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr1:174912600-174934800	Weak transcription	Left Ventricle	heart
10	chr1:174914800-174932800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr1:174919200-174926600	Enhancers	Fetal Intestine Large	intestine
12	chr1:174920800-174926200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr1:174922200-174926600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:174922800-174927200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr1:174923000-174926200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr1:174923000-174927600	Weak transcription	Right Atrium	heart
17	chr1:174923000-174933600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:174923400-174932400	Weak transcription	Fetal Heart	heart
19	chr1:174923800-174926200	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr1:174923800-174927200	Enhancers	Small Intestine	intestine
21	chr1:174924000-174926400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr1:174924000-174927600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:174924000-174932200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr1:174924000-174932400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr1:174924000-174933400	Weak transcription	Ovary	ovary
26	chr1:174924000-174933800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr1:174924000-174938200	Weak transcription	Psoas Muscle	Psoas
28	chr1:174924200-174967800	Weak transcription	Brain Germinal Matrix	brain
29	chr1:174924400-174926200	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr1:174924400-174926400	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr1:174924400-174926400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr1:174924400-174926600	Weak transcription	Duodenum Mucosa	Duodenum
33	chr1:174924400-174926800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr1:174924400-174927000	Weak transcription	Brain Anterior Caudate	brain
35	chr1:174924400-174932400	Weak transcription	Fetal Stomach	stomach
36	chr1:174924400-174933600	Weak transcription	Fetal Kidney	kidney
37	chr1:174924400-174958200	Weak transcription	Fetal Brain Male	brain
38	chr1:174924600-174926200	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr1:174924600-174926400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr1:174924600-174926400	Weak transcription	Liver	Liver
41	chr1:174924600-174926400	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr1:174924600-174926600	Weak transcription	Primary B cells from peripheral blood	blood
43	chr1:174924600-174926600	Weak transcription	Brain Substantia Nigra	brain
44	chr1:174924600-174927200	Weak transcription	K562	blood
45	chr1:174924600-174932800	Weak transcription	Primary hematopoietic stem cells	blood
46	chr1:174924600-174932800	Weak transcription	Rectal Smooth Muscle	rectum
47	chr1:174924800-174926600	Weak transcription	Brain Hippocampus Middle	brain
48	chr1:174924800-174927000	Weak transcription	Brain Cingulate Gyrus	brain
49	chr1:174924800-174932400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr1:174924800-174932600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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