Variant report

Variant	rs6697561
Chromosome Location	chr1:174861869-174861870
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 137 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:136)

rs_ID	r²[population]
rs1012182	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1034462	0.87[CHD][hapmap];0.88[JPT][hapmap]
rs10494492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs1058741	0.88[JPT][hapmap]
rs10798324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs10798327	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs10912843	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs10912853	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10912854	0.85[CEU][hapmap]
rs10912855	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11800350	0.87[EUR][1000 genomes]
rs11809803	0.85[EUR][1000 genomes]
rs11810508	0.85[EUR][1000 genomes]
rs12063093	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12078839	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12094876	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1231826	0.86[EUR][1000 genomes]
rs1231827	0.86[EUR][1000 genomes]
rs1231829	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1329281	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1613634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs1618408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1622802	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs162815	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1653630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs16847624	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap]
rs17302033	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs17302165	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs17302367	0.86[JPT][hapmap]
rs1754352	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs1754353	0.83[EUR][1000 genomes]
rs1754354	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs1754360	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17842156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17842157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs1793292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs1793294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1793298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs1793305	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs1793307	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs1793310	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1793316	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs1793318	0.82[EUR][1000 genomes]
rs1793320	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs1813136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1883139	0.88[EUR][1000 genomes]
rs1894199	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1894201	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs1894680	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap]
rs1923818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs193082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs2003378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs2146564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs2156854	0.88[JPT][hapmap]
rs2157541	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2183202	0.95[CEU][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs2760057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs2860725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs2981893	0.88[EUR][1000 genomes]
rs2981896	0.86[EUR][1000 genomes]
rs2987872	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs2987873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs2987875	0.87[EUR][1000 genomes]
rs2987876	0.85[EUR][1000 genomes]
rs2987880	0.85[EUR][1000 genomes]
rs3117838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3118982	0.88[EUR][1000 genomes]
rs3118986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs3118987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3118988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3118990	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs332763	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs332764	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs332772	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs332779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs332781	1.00[CEU][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs332784	0.85[CEU][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap]
rs332786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs332798	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs332800	0.94[CEU][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs332801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs333436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs333471	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs398350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4480415	0.88[JPT][hapmap]
rs459078	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs464635	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs4651205	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs4651231	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4651235	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4652797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs55793234	0.86[EUR][1000 genomes]
rs57289077	0.89[EUR][1000 genomes]
rs58030712	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs60482554	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6425298	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes]
rs6425300	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6425301	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6425302	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs6425303	0.81[CEU][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap]
rs6425304	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6425306	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6670315	0.90[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.90[TSI][hapmap]
rs6671196	0.87[EUR][1000 genomes]
rs6671272	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6671782	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6675528	0.81[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.83[LWK][hapmap];0.83[MKK][hapmap]
rs66836419	0.88[EUR][1000 genomes]
rs6684229	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6684515	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6686872	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6687616	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[EUR][1000 genomes]
rs6690754	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6693979	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6696465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs67133776	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs67203477	0.88[EUR][1000 genomes]
rs67903803	0.88[EUR][1000 genomes]
rs72717616	0.83[EUR][1000 genomes]
rs72717617	0.81[EUR][1000 genomes]
rs72717618	0.84[EUR][1000 genomes]
rs72717630	0.84[EUR][1000 genomes]
rs72717649	0.88[EUR][1000 genomes]
rs72717650	0.88[EUR][1000 genomes]
rs72717653	0.88[EUR][1000 genomes]
rs72717661	0.87[EUR][1000 genomes]
rs7516410	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes]
rs7521109	0.83[EUR][1000 genomes]
rs7531032	0.88[JPT][hapmap]
rs7543147	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7547658	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes]
rs913686	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs913687	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs913688	0.83[EUR][1000 genomes]
rs9425787	0.88[EUR][1000 genomes]
rs989424	0.83[EUR][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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6697561	RABGAP1L	cis	Esophagus Muscularis	GTEx
rs6697561	MRPS14	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174844800-174871600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:174844800-174874400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:174844800-174877400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:174845000-174862800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr1:174845000-174863000	Weak transcription	Primary T cells from cord blood	blood
6	chr1:174845200-174862600	Weak transcription	Liver	Liver
7	chr1:174846600-174862800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr1:174846800-174874000	Weak transcription	Ovary	ovary
9	chr1:174847000-174869200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr1:174847400-174862800	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr1:174847400-174863000	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr1:174847400-174864400	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr1:174847400-174864600	Strong transcription	H1 Cell Line	embryonic stem cell
14	chr1:174847400-174864600	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:174847600-174874400	Weak transcription	Esophagus	oesophagus
16	chr1:174849200-174864400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr1:174849600-174864400	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr1:174850200-174874800	Weak transcription	Fetal Stomach	stomach
19	chr1:174850400-174869600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:174852000-174873400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr1:174852800-174864000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr1:174852800-174874800	Weak transcription	Spleen	Spleen
23	chr1:174853400-174865000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:174853400-174870200	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr1:174854000-174862800	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr1:174854200-174862800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr1:174855600-174862400	Weak transcription	Small Intestine	intestine
28	chr1:174856400-174862600	Weak transcription	Duodenum Mucosa	Duodenum
29	chr1:174856600-174866600	Weak transcription	Primary B cells from cord blood	blood
30	chr1:174856800-174876400	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr1:174857000-174870800	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr1:174857000-174871200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:174857800-174867200	Weak transcription	Primary B cells from peripheral blood	blood
34	chr1:174858000-174871200	Weak transcription	Lung	lung
35	chr1:174859000-174868600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr1:174859000-174874000	Weak transcription	Brain Angular Gyrus	brain
37	chr1:174859400-174863000	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr1:174859400-174866600	Weak transcription	Gastric	stomach
39	chr1:174859600-174867200	Weak transcription	HepG2	liver
40	chr1:174859600-174873400	Weak transcription	K562	blood
41	chr1:174859800-174862600	Weak transcription	Stomach Mucosa	stomach
42	chr1:174860200-174868200	Weak transcription	Fetal Heart	heart
43	chr1:174861200-174863600	Strong transcription	GM12878-XiMat	blood
44	chr1:174861400-174862400	Weak transcription	Fetal Intestine Large	intestine
45	chr1:174861400-174862400	Genic enhancers	Fetal Intestine Small	intestine
46	chr1:174861400-174864400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr1:174861400-174866600	Weak transcription	Pancreas	Pancrea
48	chr1:174861400-174871200	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr1:174861400-174876200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr1:174861400-174902400	Weak transcription	Left Ventricle	heart

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