Variant report

Variant	rs1404213
Chromosome Location	chr7:102716915-102716916
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr7:102714010-102717069	SK-N-SH	brain:	n/a	chr7:102715291-102715306 chr7:102715607-102715616 chr7:102715289-102715304
2	RUNX3	chr7:102716871-102717154	GM12878	blood:	n/a	n/a
3	POLR2A	chr7:102714714-102716938	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:102715561..102717346-chr7:102754713..102757374,2	MCF-7	breast:
2	chr7:102714716..102718005-chr7:102734624..102737524,3	MCF-7	breast:
3	chr7:102714725..102717201-chr7:102788241..102791780,5	K562	blood:
4	chr6:26154807..26157784-chr7:102714627..102716921,2	MCF-7	breast:
5	chr7:102715242..102717974-chr7:105515259..105517980,2	MCF-7	breast:
6	chr7:102715629..102718160-chr7:102729461..102731149,2	K562	blood:
7	chr7:102387955..102390990-chr7:102714406..102717094,4	MCF-7	breast:
8	chr7:102714987..102719162-chr7:102758108..102764327,6	K562	blood:
9	chr7:102388357..102390801-chr7:102713734..102717426,3	K562	blood:
10	chr7:102715186..102716960-chr7:102734053..102738564,5	K562	blood:
11	chr7:102713351..102719247-chr7:102725221..102729310,7	MCF-7	breast:
12	chr7:102714022..102717631-chr7:102788669..102792237,6	MCF-7	breast:
13	chr20:53057077..53059223-chr7:102716078..102718486,2	MCF-7	breast:
14	chr17:56707584..56709248-chr7:102715096..102717010,2	MCF-7	breast:
15	chr7:102613006..102614516-chr7:102715583..102717366,2	K562	blood:
16	chr7:102714071..102718258-chr7:102757961..102760938,3	K562	blood:
17	chr7:102715186..102716937-chr7:102734053..102736983,2	K562	blood:

No data

Variant related genes	Relation type
FBXL13	TF binding region
ENSG00000161040	Chromatin interaction
ENSG00000168298	Chromatin interaction
ENSG00000222011	Chromatin interaction
ENSG00000128536	Chromatin interaction
ENSG00000170632	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000233025	Chromatin interaction
ENSG00000230257	Chromatin interaction
ENSG00000146776	Chromatin interaction
ENSG00000161048	Chromatin interaction

Extended variants
information (count: 150 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:147)

rs_ID	r²[population]
rs10229137	1.00[EUR][1000 genomes]
rs10230292	1.00[EUR][1000 genomes]
rs10232494	0.85[AMR][1000 genomes]
rs10240086	1.00[EUR][1000 genomes]
rs10260344	1.00[EUR][1000 genomes]
rs10264869	1.00[EUR][1000 genomes]
rs10268112	1.00[EUR][1000 genomes]
rs10268849	1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs10278727	1.00[MEX][hapmap]
rs10808121	1.00[MEX][hapmap]
rs10808122	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs10808123	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10808124	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10808125	0.80[YRI][hapmap];1.00[EUR][1000 genomes]
rs10808127	1.00[EUR][1000 genomes]
rs11560367	1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[EUR][1000 genomes]
rs11760826	1.00[EUR][1000 genomes]
rs11765948	1.00[EUR][1000 genomes]
rs11772979	1.00[EUR][1000 genomes]
rs11773883	1.00[EUR][1000 genomes]
rs11981558	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12155099	1.00[EUR][1000 genomes]
rs12539639	1.00[EUR][1000 genomes]
rs13225565	0.91[YRI][hapmap];1.00[EUR][1000 genomes]
rs13226097	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13242079	0.81[ASW][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13247932	1.00[EUR][1000 genomes]
rs1477159	1.00[EUR][1000 genomes]
rs1477160	0.86[ASW][hapmap];1.00[MEX][hapmap]
rs1477161	1.00[EUR][1000 genomes]
rs1477162	1.00[EUR][1000 genomes]
rs1477163	1.00[EUR][1000 genomes]
rs1543987	1.00[MEX][hapmap]
rs1558853	0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1861725	1.00[EUR][1000 genomes]
rs1861726	1.00[EUR][1000 genomes]
rs1861728	0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1861730	0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1861732	1.00[EUR][1000 genomes]
rs1968198	1.00[EUR][1000 genomes]
rs1968199	0.88[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.80[YRI][hapmap];1.00[EUR][1000 genomes]
rs1968202	1.00[EUR][1000 genomes]
rs1974715	1.00[EUR][1000 genomes]
rs1974716	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2015289	1.00[EUR][1000 genomes]
rs2041949	0.81[ASW][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2098447	1.00[EUR][1000 genomes]
rs2111381	1.00[EUR][1000 genomes]
rs2140621	1.00[MEX][hapmap]
rs2177550	1.00[MEX][hapmap]
rs2193418	0.87[ASW][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2411079	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2411081	1.00[EUR][1000 genomes]
rs2411082	1.00[EUR][1000 genomes]
rs28881872	1.00[MEX][hapmap]
rs2898638	1.00[MEX][hapmap]
rs2898640	1.00[EUR][1000 genomes]
rs3181009	0.85[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[EUR][1000 genomes]
rs4295594	1.00[EUR][1000 genomes]
rs4530973	1.00[EUR][1000 genomes]
rs4576360	1.00[MEX][hapmap]
rs4727558	1.00[MEX][hapmap]
rs4727560	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4727561	1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs4729868	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4729869	1.00[EUR][1000 genomes]
rs4729870	0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4729871	0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4729872	0.93[ASW][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4729874	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4729875	0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4729876	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4729878	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4729882	0.80[YRI][hapmap];1.00[EUR][1000 genomes]
rs4729883	1.00[EUR][1000 genomes]
rs4729884	1.00[EUR][1000 genomes]
rs4729892	1.00[EUR][1000 genomes]
rs5025411	0.80[ASW][hapmap];0.80[LWK][hapmap]
rs56938507	1.00[EUR][1000 genomes]
rs61187383	1.00[EUR][1000 genomes]
rs61676871	1.00[EUR][1000 genomes]
rs62622397	1.00[EUR][1000 genomes]
rs6465883	1.00[MEX][hapmap]
rs6465888	1.00[MEX][hapmap]
rs6465890	0.89[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.83[YRI][hapmap]
rs6465891	1.00[EUR][1000 genomes]
rs6465892	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6465898	0.80[YRI][hapmap];1.00[EUR][1000 genomes]
rs6465902	1.00[EUR][1000 genomes]
rs6465905	1.00[EUR][1000 genomes]
rs6465907	1.00[EUR][1000 genomes]
rs6465911	1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs6944809	1.00[EUR][1000 genomes]
rs6945578	1.00[EUR][1000 genomes]
rs6946968	0.80[YRI][hapmap];1.00[EUR][1000 genomes]
rs6946989	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6947777	1.00[EUR][1000 genomes]
rs6950177	1.00[ASW][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6955436	1.00[EUR][1000 genomes]
rs6958533	1.00[MEX][hapmap]
rs6959711	1.00[EUR][1000 genomes]
rs6964822	1.00[EUR][1000 genomes]
rs6966872	0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6966961	0.80[YRI][hapmap];1.00[EUR][1000 genomes]
rs6968559	1.00[EUR][1000 genomes]
rs6973702	0.86[ASW][hapmap];1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs6973787	1.00[EUR][1000 genomes]
rs6976034	0.80[YRI][hapmap];1.00[EUR][1000 genomes]
rs6976290	1.00[EUR][1000 genomes]
rs6976794	0.80[YRI][hapmap];1.00[EUR][1000 genomes]
rs6977206	1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs6979140	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6979470	1.00[EUR][1000 genomes]
rs73408205	1.00[EUR][1000 genomes]
rs73408207	1.00[EUR][1000 genomes]
rs73408209	1.00[EUR][1000 genomes]
rs73408210	1.00[EUR][1000 genomes]
rs73408223	1.00[EUR][1000 genomes]
rs73408251	1.00[EUR][1000 genomes]
rs73408254	1.00[EUR][1000 genomes]
rs73408255	1.00[EUR][1000 genomes]
rs73408259	1.00[EUR][1000 genomes]
rs73408285	1.00[EUR][1000 genomes]
rs73408286	1.00[EUR][1000 genomes]
rs73410119	1.00[EUR][1000 genomes]
rs73410129	1.00[EUR][1000 genomes]
rs73410143	1.00[EUR][1000 genomes]
rs7341515	1.00[MEX][hapmap]
rs7349957	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7350051	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7782147	1.00[EUR][1000 genomes]
rs7783856	1.00[ASW][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7784337	1.00[ASW][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7792240	0.80[YRI][hapmap];1.00[EUR][1000 genomes]
rs7804020	0.80[ASW][hapmap]
rs7805950	1.00[MEX][hapmap]
rs7806136	1.00[MEX][hapmap]
rs7806691	1.00[MEX][hapmap]
rs7807900	1.00[EUR][1000 genomes]
rs7809075	1.00[MEX][hapmap]
rs847650	1.00[MEX][hapmap]
rs847653	1.00[MEX][hapmap]
rs9640672	1.00[EUR][1000 genomes]
rs9641307	1.00[EUR][1000 genomes]
rs9641308	1.00[EUR][1000 genomes]
rs9649257	0.82[AFR][1000 genomes]
rs9691829	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868996	chr7:102332827-102991361	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS 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 miRNA target site	46 gene(s)	inside rSNPs	diseases
2	esv2752138	chr7:102358320-102787135	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv526764	chr7:102701826-102737251	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1404213	SVH	cis	multi-tissue	Pritchard
rs1404213	ARMC10	cis	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102714000-102717000	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr7:102714200-102717000	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr7:102714200-102717000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr7:102714200-102717000	Active TSS	A549	lung
5	chr7:102714400-102717000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr7:102714600-102717000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr7:102714800-102717000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr7:102714800-102717000	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr7:102714800-102717000	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr7:102714800-102717000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr7:102715000-102717600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr7:102716000-102717000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
13	chr7:102716000-102717000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr7:102716000-102717000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr7:102716000-102717000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr7:102716000-102717000	Flanking Active TSS	Dnd41	blood
17	chr7:102716000-102717600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr7:102716200-102717000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr7:102716200-102717000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr7:102716200-102717000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr7:102716200-102717000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr7:102716200-102717000	Flanking Active TSS	Brain Anterior Caudate	brain
23	chr7:102716200-102717000	Flanking Active TSS	Brain Hippocampus Middle	brain
24	chr7:102716200-102717000	Flanking Active TSS	Brain Substantia Nigra	brain
25	chr7:102716200-102717000	Flanking Active TSS	Hela-S3	cervix
26	chr7:102716200-102717000	Flanking Active TSS	HUVEC	blood vessel
27	chr7:102716200-102717000	Flanking Active TSS	K562	blood
28	chr7:102716200-102717000	Flanking Active TSS	Osteobl	bone
29	chr7:102716400-102717000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
30	chr7:102716400-102717000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
31	chr7:102716400-102717000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr7:102716400-102717000	Flanking Active TSS	Brain Angular Gyrus	brain
33	chr7:102716400-102717000	Flanking Active TSS	Fetal Brain Female	brain
34	chr7:102716400-102717000	Flanking Active TSS	Rectal Smooth Muscle	rectum
35	chr7:102716400-102717400	Weak transcription	Gastric	stomach
36	chr7:102716400-102717600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
37	chr7:102716400-102723600	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr7:102716400-102734000	Weak transcription	Esophagus	oesophagus
39	chr7:102716400-102745400	Weak transcription	Spleen	Spleen
40	chr7:102716600-102717000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr7:102716600-102717000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr7:102716600-102717000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr7:102716600-102717000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr7:102716600-102717000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr7:102716600-102717000	Flanking Active TSS	HepG2	liver
46	chr7:102716600-102717000	Flanking Active TSS	NHLF	lung
47	chr7:102716600-102717400	Enhancers	Fetal Muscle Trunk	muscle
48	chr7:102716600-102717600	Enhancers	Primary B cells from peripheral blood	blood
49	chr7:102716600-102717600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
50	chr7:102716600-102717600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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