Variant report

Variant	rs548994
Chromosome Location	chr7:112556307-112556308
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:112551586..112554572-chr7:112556093..112557637,2	MCF-7	breast:
2	chr7:112421578..112423451-chr7:112555426..112557835,2	MCF-7	breast:
3	chr7:112544252..112546873-chr7:112556132..112557690,2	MCF-7	breast:
4	chr7:112548050..112550695-chr7:112555857..112557634,3	MCF-7	breast:
5	chr7:112555338..112557773-chr7:112577965..112581665,4	MCF-7	breast:
6	chr7:112554744..112557418-chr7:112564931..112568212,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164603	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10237980	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10246678	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10261874	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1227171	0.94[CEU][hapmap]
rs1227174	0.95[CEU][hapmap]
rs1227190	0.95[CEU][hapmap]
rs1238698	0.94[CEU][hapmap]
rs12535487	0.90[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12539085	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1533851	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1547554	0.95[CEU][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs1718944	0.85[YRI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1718948	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1718961	0.89[EUR][1000 genomes]
rs1718967	0.95[CEU][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs1796492	0.95[CEU][hapmap]
rs1796493	0.95[CEU][hapmap]
rs1796512	0.87[EUR][1000 genomes]
rs1796516	0.95[CEU][hapmap]
rs1996843	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs2396573	0.90[EUR][1000 genomes]
rs2396574	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2457	0.95[CEU][hapmap]
rs2687267	0.95[CEU][hapmap];0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2708295	0.87[EUR][1000 genomes]
rs2708296	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs35548417	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3997335	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs3997336	0.90[EUR][1000 genomes]
rs494324	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs549688	0.95[CEU][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs552304	0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs564494	1.00[CEU][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs565641	0.85[EUR][1000 genomes]
rs62472532	0.80[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6466421	0.90[CEU][hapmap]
rs660743	0.85[YRI][hapmap]
rs672911	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs685259	1.00[CEU][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6948575	0.85[EUR][1000 genomes]
rs6953522	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6967716	0.88[EUR][1000 genomes]
rs7785774	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7803405	0.95[CEU][hapmap]
rs821782	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs821783	1.00[CEU][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs821785	0.95[CEU][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs821787	0.95[CEU][hapmap];0.94[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9969347	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531436	chr7:111856171-112585407	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	105 gene(s)	inside rSNPs	diseases
2	esv1794529	chr7:112400060-112588376	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	esv2754368	chr7:112483049-112588049	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv2758131	chr7:112492127-112768628	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv2759556	chr7:112492127-112768628	Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:112507400-112556800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr7:112519000-112557400	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr7:112522200-112571000	Weak transcription	Thymus	Thymus
4	chr7:112522400-112558400	Weak transcription	Gastric	stomach
5	chr7:112522400-112558800	Weak transcription	Lung	lung
6	chr7:112524200-112556800	Weak transcription	Colonic Mucosa	Colon
7	chr7:112530400-112576600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr7:112538800-112565600	Weak transcription	Pancreas	Pancrea
9	chr7:112539000-112559400	Weak transcription	Fetal Stomach	stomach
10	chr7:112541400-112578800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr7:112543000-112557000	Weak transcription	HepG2	liver
12	chr7:112546400-112566000	Weak transcription	Right Ventricle	heart
13	chr7:112548600-112556800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr7:112548800-112556400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr7:112548800-112556400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr7:112549000-112557400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr7:112549200-112569000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr7:112549200-112571000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr7:112549400-112574200	Weak transcription	Fetal Brain Female	brain
20	chr7:112549600-112556400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr7:112549600-112565800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr7:112550400-112560200	Weak transcription	HUVEC	blood vessel
23	chr7:112551400-112556400	Weak transcription	Fetal Intestine Small	intestine
24	chr7:112551400-112566200	Weak transcription	Aorta	Aorta
25	chr7:112551600-112556400	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr7:112551600-112556400	Weak transcription	Duodenum Mucosa	Duodenum
27	chr7:112551600-112556400	Weak transcription	K562	blood
28	chr7:112551600-112556800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr7:112551600-112556800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr7:112551600-112556800	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr7:112551600-112557200	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr7:112551600-112557200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr7:112551600-112558400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr7:112551600-112558400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr7:112551600-112558400	Weak transcription	Fetal Kidney	kidney
36	chr7:112551600-112558400	Weak transcription	Osteobl	bone
37	chr7:112551600-112559400	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr7:112551600-112559400	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr7:112551600-112563800	Weak transcription	Stomach Smooth Muscle	stomach
40	chr7:112551600-112565800	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr7:112551600-112571000	Weak transcription	HSMM	muscle
42	chr7:112551600-112575600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr7:112551600-112575800	Weak transcription	GM12878-XiMat	blood
44	chr7:112551600-112576200	Weak transcription	Ovary	ovary
45	chr7:112551600-112577400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr7:112551600-112578600	Weak transcription	Fetal Muscle Trunk	muscle
47	chr7:112551600-112579400	Weak transcription	Spleen	Spleen
48	chr7:112551800-112564400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr7:112552000-112557000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr7:112552000-112557600	Weak transcription	Liver	Liver

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