Variant report

Variant	rs893258
Chromosome Location	chr2:73219922-73219923
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr2:73219920-73220070	HAc	cerebellar:	n/a	n/a
2	SMC3	chr2:73219890-73221152	SK-N-SH	brain:	n/a	chr2:73220384-73220398
3	CTCF	chr2:73219860-73220010	SAEC	small airway:	n/a	n/a
4	CTCF	chr2:73219840-73219990	GM12873	blood:	n/a	n/a
5	CTCF	chr2:73219886-73220814	A549	lung:	n/a	chr2:73220384-73220405 chr2:73220385-73220394 chr2:73220387-73220397 chr2:73220385-73220398 chr2:73220383-73220399 chr2:73220382-73220400
6	CTCF	chr2:73219900-73220050	GM12867	blood:	n/a	n/a
7	CTCF	chr2:73219840-73219990	HCT-116	colon:	n/a	n/a
8	CTCF	chr2:73219900-73220050	GM12871	blood:	n/a	n/a
9	CTCF	chr2:73219800-73219950	AG09319	gingival:	n/a	n/a
10	CTCF	chr2:73219840-73219990	HVMF	connective:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:73219903..73220480-chr2:73383337..73384344,3	MCF-7	breast:
2	chr2:73218132..73222464-chr2:73296356..73300991,4	K562	blood:
3	chr2:73219841..73220628-chr2:73404226..73405455,7	K562	blood:
4	chr2:73219860..73220941-chr2:73304787..73305824,5	MCF-7	breast:
5	chr2:73219221..73222584-chr2:73297203..73300121,3	MCF-7	breast:
6	chr2:73219903..73221030-chr2:73390442..73391587,9	K562	blood:
7	chr2:73219754..73220799-chr2:73390573..73391231,4	MCF-7	breast:
8	chr2:73217756..73221596-chr2:73297435..73299789,3	MCF-7	breast:
9	chr2:73219831..73220418-chr2:73439379..73440278,2	K562	blood:
10	chr2:73200598..73201336-chr2:73219886..73220414,2	K562	blood:
11	chr2:73218132..73220695-chr2:73298019..73300991,2	K562	blood:

Variant related genes	Relation type
SFXN5	TF binding region
ENSG00000144040	Chromatin interaction
ENSG00000135631	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10166058	0.86[ASN][1000 genomes]
rs10166220	0.82[CHB][hapmap];0.96[JPT][hapmap];0.83[ASN][1000 genomes]
rs10167566	0.91[JPT][hapmap]
rs10174548	0.87[JPT][hapmap]
rs10176939	0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10177159	0.81[CHB][hapmap];0.96[JPT][hapmap];0.91[ASN][1000 genomes]
rs10178854	0.83[ASN][1000 genomes]
rs10178944	0.83[ASN][1000 genomes]
rs10180720	0.90[JPT][hapmap]
rs10180995	0.90[JPT][hapmap]
rs10189744	0.82[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs10190861	0.91[JPT][hapmap]
rs10191665	0.81[ASN][1000 genomes]
rs10192077	0.86[CHD][hapmap];0.95[JPT][hapmap]
rs10197305	0.87[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10209859	0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs1036512	0.85[ASN][1000 genomes]
rs12233055	0.86[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs12621323	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13388404	0.82[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs13400920	0.86[JPT][hapmap]
rs13400948	0.81[JPT][hapmap]
rs13403757	0.87[JPT][hapmap]
rs13403781	0.87[JPT][hapmap]
rs13416407	0.83[JPT][hapmap]
rs13424057	0.81[ASN][1000 genomes]
rs1370383	0.86[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs1430349	0.86[JPT][hapmap]
rs17008571	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17008611	0.86[JPT][hapmap]
rs17008631	0.87[JPT][hapmap]
rs1864488	0.86[JPT][hapmap]
rs1992133	0.85[JPT][hapmap]
rs2421098	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3813222	0.91[JPT][hapmap]
rs3901273	0.86[JPT][hapmap]
rs4144837	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs4514897	0.87[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4527230	0.92[ASN][1000 genomes]
rs58993488	0.92[ASN][1000 genomes]
rs61161134	0.85[ASN][1000 genomes]
rs61650913	0.86[ASN][1000 genomes]
rs62147721	0.90[ASN][1000 genomes]
rs62147724	0.90[ASN][1000 genomes]
rs6546794	0.92[ASN][1000 genomes]
rs6546796	0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs6546797	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs6546800	0.86[JPT][hapmap]
rs6709938	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6710362	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6710739	0.90[JPT][hapmap]
rs6710755	0.81[JPT][hapmap]
rs6711891	0.87[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs6713655	0.81[ASN][1000 genomes]
rs6717553	0.81[ASN][1000 genomes]
rs6719333	0.82[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs6726940	0.86[CHB][hapmap];0.96[JPT][hapmap];0.92[ASN][1000 genomes]
rs6727919	0.86[JPT][hapmap]
rs6729266	0.86[JPT][hapmap]
rs6732369	0.83[CHD][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs6736153	0.86[JPT][hapmap]
rs6749237	0.91[JPT][hapmap]
rs6750069	0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6754779	0.81[ASN][1000 genomes]
rs6754858	0.81[ASN][1000 genomes]
rs6757131	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6759243	0.84[ASN][1000 genomes]
rs6759733	0.85[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs727470	0.86[JPT][hapmap]
rs732178	0.85[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs732179	0.86[CHB][hapmap];0.96[JPT][hapmap];0.89[ASN][1000 genomes]
rs732180	0.86[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs7557173	0.86[JPT][hapmap]
rs7559340	0.85[JPT][hapmap]
rs7566904	0.90[JPT][hapmap]
rs7570876	0.82[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs7578757	0.90[ASN][1000 genomes]
rs7579770	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7580216	0.86[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs7597032	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7602651	0.86[JPT][hapmap]
rs891432	0.86[JPT][hapmap]
rs891433	0.85[JPT][hapmap]
rs893259	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9309467	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874266	chr2:73137991-73220138	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1002295	chr2:73216155-73350391	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs893258	RAB11FIP5	cis	multi-tissue	Pritchard

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73168800-73226800	Weak transcription	NHLF	lung
2	chr2:73176600-73227400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:73183200-73228200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr2:73190600-73234400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:73193600-73221200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr2:73194200-73248800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:73198600-73220000	Weak transcription	Small Intestine	intestine
8	chr2:73207800-73263200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr2:73208000-73247600	Weak transcription	Primary B cells from cord blood	blood
10	chr2:73208200-73227000	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr2:73208400-73227400	Weak transcription	A549	lung
12	chr2:73208400-73227600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr2:73208600-73227200	Weak transcription	Colon Smooth Muscle	Colon
14	chr2:73209000-73227000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr2:73209000-73227200	Weak transcription	HSMM	muscle
16	chr2:73210400-73227200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr2:73210600-73225400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr2:73211000-73258400	Weak transcription	Colonic Mucosa	Colon
19	chr2:73211600-73221800	Weak transcription	Fetal Brain Male	brain
20	chr2:73211600-73235800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr2:73212000-73223000	Weak transcription	Brain Angular Gyrus	brain
22	chr2:73212000-73225400	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr2:73212200-73247400	Weak transcription	HSMMtube	muscle
24	chr2:73212400-73227400	Weak transcription	Adipose Nuclei	Adipose
25	chr2:73212400-73236000	Weak transcription	Esophagus	oesophagus
26	chr2:73212800-73238800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr2:73213800-73220400	Weak transcription	K562	blood
28	chr2:73213800-73221800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:73213800-73222600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr2:73213800-73227400	Weak transcription	Gastric	stomach
31	chr2:73213800-73236200	Weak transcription	Pancreas	Pancrea
32	chr2:73214000-73220200	Strong transcription	Fetal Intestine Small	intestine
33	chr2:73214000-73222000	Weak transcription	Fetal Thymus	thymus
34	chr2:73214000-73232000	Weak transcription	Aorta	Aorta
35	chr2:73214000-73238400	Weak transcription	Fetal Lung	lung
36	chr2:73214200-73225600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr2:73214200-73247800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr2:73214200-73286400	Weak transcription	Psoas Muscle	Psoas
39	chr2:73215200-73228400	Weak transcription	Placenta	Placenta
40	chr2:73215400-73220200	Weak transcription	Brain Anterior Caudate	brain
41	chr2:73215400-73236000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr2:73215800-73223800	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr2:73215800-73235600	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr2:73215800-73247400	Weak transcription	Thymus	Thymus
45	chr2:73215800-73263000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr2:73216000-73220000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr2:73216000-73220200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr2:73216000-73223000	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr2:73216000-73236000	Weak transcription	Duodenum Mucosa	Duodenum
50	chr2:73216200-73220000	Weak transcription	Brain Substantia Nigra	brain

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