Variant report

Variant	rs7559340
Chromosome Location	chr2:73314309-73314310
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	SMC3	chr2:73312373-73314464	SK-N-SH	brain:	n/a	chr2:73312933-73312947 chr2:73313348-73313358

No.	Distal block	Cell Line	Cell type
1	chr2:73295399..73297749-chr2:73313292..73315077,2	MCF-7	breast:
2	chr2:73313142..73315142-chr2:73381428..73383414,2	K562	blood:
3	chr2:73312133..73315047-chr2:73386146..73388493,2	K562	blood:
4	chr2:73312164..73314487-chr2:73402908..73404821,2	K562	blood:

Variant related genes	Relation type
RAB11FIP5	TF binding region
ENSG00000144040	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10166220	0.81[CEU][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes]
rs10167566	0.80[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10174548	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10176939	0.81[CEU][hapmap];0.85[JPT][hapmap];0.89[YRI][hapmap]
rs10177159	0.80[JPT][hapmap]
rs10178944	0.83[AMR][1000 genomes]
rs10180720	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10180995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10189744	0.81[CEU][hapmap];0.90[JPT][hapmap]
rs10190861	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10192077	0.81[CEU][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10197305	0.80[GIH][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap]
rs10203608	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1036512	0.82[AMR][1000 genomes]
rs1046186	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10865396	0.86[ASN][1000 genomes]
rs11126389	0.86[ASN][1000 genomes]
rs11686557	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11885522	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12104691	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12233055	0.81[CEU][hapmap];0.80[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap]
rs12614059	0.90[ASN][1000 genomes]
rs13018842	0.86[ASN][1000 genomes]
rs13385994	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13388404	0.90[JPT][hapmap]
rs13390072	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13391532	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13393567	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13400920	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13400948	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.82[YRI][hapmap];0.94[ASN][1000 genomes]
rs13403757	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13403781	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13407719	0.94[ASN][1000 genomes]
rs13416407	0.94[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13427947	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1370383	0.82[GIH][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap]
rs1430349	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1430350	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1430351	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17008571	0.85[JPT][hapmap];0.89[YRI][hapmap]
rs17008611	0.82[GIH][hapmap];0.81[JPT][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap]
rs17008631	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1864488	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[ASN][1000 genomes]
rs1992133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2421098	0.90[JPT][hapmap]
rs35131031	0.83[ASN][1000 genomes]
rs3813222	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3813223	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3901273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4144837	0.87[CEU][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4514897	0.90[JPT][hapmap]
rs4591365	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55894650	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55974516	0.82[AMR][1000 genomes]
rs57536428	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57701326	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs57726945	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57937746	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61161134	0.82[AMR][1000 genomes]
rs6546796	0.82[GIH][hapmap];0.80[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.81[YRI][hapmap]
rs6546797	0.82[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs6546800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6546801	0.94[ASN][1000 genomes]
rs6709938	0.85[JPT][hapmap]
rs6710739	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6710755	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6711891	0.85[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.87[YRI][hapmap]
rs6712925	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6713655	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6719333	0.81[CEU][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes]
rs6720817	0.95[ASN][1000 genomes]
rs6726940	0.80[JPT][hapmap]
rs6727269	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6727919	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6729266	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.96[ASN][1000 genomes]
rs6732369	0.82[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes]
rs6736153	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[ASN][1000 genomes]
rs6749237	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6750069	0.81[CEU][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap]
rs6754779	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6754858	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6757131	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs6759733	0.81[CEU][hapmap];0.80[JPT][hapmap];0.86[MEX][hapmap]
rs727470	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs727471	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs732178	0.81[CEU][hapmap]
rs732179	0.81[CEU][hapmap];0.80[JPT][hapmap]
rs732180	0.81[CEU][hapmap];0.80[GIH][hapmap];0.80[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap]
rs7557173	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7559074	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7566904	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7570876	0.90[JPT][hapmap];0.93[YRI][hapmap];0.81[AMR][1000 genomes]
rs7579770	0.85[JPT][hapmap]
rs7580216	0.81[CEU][hapmap];0.80[GIH][hapmap];0.80[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap]
rs7593322	0.96[ASN][1000 genomes]
rs7597032	0.85[JPT][hapmap]
rs7599657	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7602651	0.87[CEU][hapmap];0.95[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs891432	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs891433	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs893258	0.85[JPT][hapmap]
rs893259	0.85[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.80[YRI][hapmap]
rs9309471	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[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	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
2	nsv1006801	chr2:73305056-73431711	Weak transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73299200-73314800	Weak transcription	Small Intestine	intestine
2	chr2:73299400-73314800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr2:73299400-73314800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr2:73299400-73318200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr2:73299400-73318400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:73299600-73314600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr2:73299600-73314800	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr2:73299600-73315400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr2:73299600-73316000	Weak transcription	NHDF-Ad	bronchial
10	chr2:73299600-73319400	Weak transcription	K562	blood
11	chr2:73299800-73314800	Weak transcription	Brain Substantia Nigra	brain
12	chr2:73299800-73314800	Weak transcription	HSMM	muscle
13	chr2:73300000-73319200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr2:73302600-73316400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:73303000-73328600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr2:73303200-73320600	Weak transcription	Psoas Muscle	Psoas
17	chr2:73303400-73320000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr2:73306600-73314800	Weak transcription	HMEC	breast
19	chr2:73307400-73314400	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr2:73307800-73314800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr2:73308400-73314400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr2:73309000-73314400	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr2:73309200-73314600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr2:73309200-73316200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr2:73309200-73319400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr2:73309600-73316600	Strong transcription	HepG2	liver
27	chr2:73309800-73315600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr2:73310000-73315200	Genic enhancers	Fetal Muscle Leg	muscle
29	chr2:73310800-73316400	Genic enhancers	Fetal Muscle Trunk	muscle
30	chr2:73311000-73316400	Genic enhancers	Stomach Smooth Muscle	stomach
31	chr2:73311400-73314600	Weak transcription	Colonic Mucosa	Colon
32	chr2:73311400-73316000	Strong transcription	Osteobl	bone
33	chr2:73311600-73315800	Strong transcription	NHLF	lung
34	chr2:73311800-73315400	Enhancers	Placenta Amnion	Placenta Amnion
35	chr2:73311800-73316400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr2:73312000-73316000	Strong transcription	Gastric	stomach
37	chr2:73312200-73314600	Weak transcription	Duodenum Mucosa	Duodenum
38	chr2:73312200-73316200	Strong transcription	Brain Germinal Matrix	brain
39	chr2:73312200-73316600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr2:73312400-73314400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr2:73312600-73315000	Weak transcription	A549	lung
42	chr2:73312600-73315800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr2:73312600-73316400	Weak transcription	Hela-S3	cervix
44	chr2:73312800-73315800	Strong transcription	NHEK	skin
45	chr2:73312800-73316200	Weak transcription	Right Atrium	heart
46	chr2:73313000-73316000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr2:73313000-73316200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr2:73313000-73317400	Genic enhancers	Spleen	Spleen
49	chr2:73313000-73319000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr2:73313200-73314600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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