Variant report

Variant	rs2688198
Chromosome Location	chr5:154256714-154256715
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:154236696..154239657-chr5:154255022..154258392,4	MCF-7	breast:
2	chr5:154255319..154256934-chr5:154260539..154262429,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155508	Chromatin interaction
ENSG00000170271	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1035368	1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10515727	1.00[CHB][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap]
rs12187921	1.00[TSI][hapmap]
rs12188498	1.00[CHB][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap]
rs12188828	1.00[CEU][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.85[EUR][1000 genomes]
rs12188906	1.00[CHB][hapmap]
rs12300	0.93[ASW][hapmap];0.87[CEU][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1421814	1.00[CHB][hapmap]
rs1421815	1.00[CHB][hapmap];1.00[TSI][hapmap]
rs1421819	1.00[CHB][hapmap];1.00[TSI][hapmap]
rs164195	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17096232	1.00[CHB][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap]
rs17116409	1.00[TSI][hapmap]
rs17116411	0.85[EUR][1000 genomes]
rs17116414	0.85[EUR][1000 genomes]
rs17116417	1.00[CHB][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap]
rs17116421	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.85[EUR][1000 genomes]
rs17116442	0.93[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17116455	1.00[CHB][hapmap]
rs17116489	1.00[CHB][hapmap]
rs17116534	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17116638	1.00[CHB][hapmap]
rs180846	1.00[CEU][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs186971	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1974776	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.97[LWK][hapmap];0.89[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1974777	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.97[LWK][hapmap];0.89[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2042168	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2112223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2161128	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2258437	1.00[ASW][hapmap];0.93[CEU][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.95[LWK][hapmap];0.84[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2291780	1.00[CHB][hapmap]
rs2396999	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs2544859	0.93[CEU][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2544860	0.86[JPT][hapmap]
rs2544866	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2544874	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2544875	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2544876	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2544880	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.97[LWK][hapmap];0.89[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2544884	1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2560063	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2644743	1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2644744	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2644746	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2688186	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2688187	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688188	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2688189	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2688190	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688191	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2688193	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2688194	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2688195	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2688199	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688200	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2688201	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2688206	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32427	0.86[JPT][hapmap]
rs348739	1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs348748	1.00[CEU][hapmap];0.96[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs348749	0.86[CEU][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs348750	0.87[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs348751	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs348752	0.93[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.97[LWK][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs348754	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3776984	1.00[CHB][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap]
rs39614	0.93[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4354100	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4958771	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55770418	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56374414	0.87[EUR][1000 genomes]
rs58415346	0.85[EUR][1000 genomes]
rs59525998	0.87[EUR][1000 genomes]
rs59749917	0.87[EUR][1000 genomes]
rs6865950	1.00[CHB][hapmap];1.00[TSI][hapmap]
rs6879277	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6884416	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6895741	1.00[CHB][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap]
rs702742	1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73276742	0.85[EUR][1000 genomes]
rs73280705	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7716019	1.00[CHB][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap]
rs7723269	0.85[EUR][1000 genomes]
rs7728194	0.82[EUR][1000 genomes]
rs816717	0.93[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs816718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs816720	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs816722	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs816743	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs816747	0.86[JPT][hapmap]
rs888694	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs960499	0.86[JPT][hapmap]
rs9942412	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2688198	ANXA6	cis	parietal	SCAN
rs2688198	EBF1	cis	parietal	SCAN
rs2688198	CCDC69	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154239600-154263800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:154240600-154264800	Weak transcription	Stomach Mucosa	stomach
3	chr5:154240800-154256800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr5:154242000-154256800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:154242000-154257600	Strong transcription	Fetal Thymus	thymus
6	chr5:154242200-154256800	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr5:154242200-154256800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr5:154242400-154257000	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr5:154242400-154257000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr5:154242400-154257600	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr5:154242400-154257600	Strong transcription	Liver	Liver
12	chr5:154242800-154256800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr5:154242800-154256800	Strong transcription	Placenta	Placenta
14	chr5:154242800-154257000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr5:154242800-154257000	Strong transcription	HUVEC	blood vessel
16	chr5:154242800-154257200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr5:154242800-154257600	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr5:154243200-154257000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr5:154243200-154257200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr5:154243200-154257200	Strong transcription	Duodenum Smooth Muscle	Duodenum
21	chr5:154243200-154257600	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr5:154243400-154256800	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr5:154243400-154257000	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr5:154243400-154257200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr5:154243600-154257200	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr5:154243800-154257400	Strong transcription	Dnd41	blood
27	chr5:154244600-154257600	Strong transcription	Primary B cells from peripheral blood	blood
28	chr5:154247400-154257200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr5:154248000-154256800	Strong transcription	Primary T cells from cord blood	blood
30	chr5:154248000-154256800	Strong transcription	Thymus	Thymus
31	chr5:154248000-154257000	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr5:154248000-154257400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr5:154248200-154257000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr5:154248200-154257400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr5:154248400-154256800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr5:154248600-154256800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr5:154248600-154257000	Strong transcription	Fetal Muscle Leg	muscle
38	chr5:154248600-154257600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr5:154248600-154257800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr5:154248600-154267600	Weak transcription	Right Atrium	heart
41	chr5:154249200-154257000	Strong transcription	Primary hematopoietic stem cells	blood
42	chr5:154249200-154257200	Strong transcription	A549	lung
43	chr5:154249200-154257400	Strong transcription	Fetal Muscle Trunk	muscle
44	chr5:154249400-154256800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr5:154249600-154257200	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr5:154249600-154257400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr5:154249600-154257600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr5:154249600-154257600	Strong transcription	Fetal Intestine Large	intestine
49	chr5:154249600-154257800	Strong transcription	Primary B cells from cord blood	blood
50	chr5:154249600-154259000	Strong transcription	HSMM	muscle

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