Variant report

Variant	rs13416407
Chromosome Location	chr2:73312005-73312006
allele	A/C
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	POLR2A	chr2:73311807-73312032	HUVEC	blood vessel:	n/a	n/a
2	CTCF	chr2:73311873-73313353	A549	lung:	n/a	chr2:73312936-73312944 chr2:73313039-73313052 chr2:73312933-73312954 chr2:73312931-73312949 chr2:73312932-73312948
3	MYC	chr2:73311940-73312092	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:73306420..73310594-chr2:73310994..73314109,4	K562	blood:
2	chr2:73311681..73313517-chr2:73382261..73385260,2	MCF-7	breast:
3	chr2:73296621..73300316-chr2:73309682..73312950,4	K562	blood:
4	chr2:73311975..73313596-chr2:73382382..73383895,2	MCF-7	breast:
5	chr2:73311857..73313371-chr2:73390449..73391577,9	K562	blood:

Variant related genes	Relation type
RAB11FIP5	TF binding region
ENSG00000144040	Chromatin interaction
ENSG00000135631	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10166220	0.87[JPT][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes]
rs10167566	1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10174548	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10176939	0.83[JPT][hapmap];0.89[YRI][hapmap]
rs10178944	0.83[AMR][1000 genomes]
rs10180720	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10180995	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10189744	0.86[JPT][hapmap]
rs10190861	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10192077	0.81[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10197305	0.81[JPT][hapmap]
rs10203608	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1036512	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1046186	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10865396	0.86[ASN][1000 genomes]
rs11126389	0.86[ASN][1000 genomes]
rs11686557	0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs11885522	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12104691	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12614059	0.89[ASN][1000 genomes]
rs13018842	0.86[ASN][1000 genomes]
rs13385994	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13388404	0.86[JPT][hapmap]
rs13390072	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13391532	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13393567	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13400920	0.87[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13400948	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.82[YRI][hapmap];0.95[ASN][1000 genomes]
rs13403757	1.00[CHB][hapmap];0.87[JPT][hapmap];0.95[ASN][1000 genomes]
rs13403781	1.00[CHB][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs13407719	0.95[ASN][1000 genomes]
rs13427947	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1430349	0.94[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1430350	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1430351	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17008571	0.83[JPT][hapmap];0.89[YRI][hapmap]
rs17008631	0.83[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1864488	0.95[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs1992133	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2421098	0.86[JPT][hapmap]
rs35131031	0.82[ASN][1000 genomes]
rs3813222	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813223	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3901273	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4144837	0.83[CEU][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4514897	0.86[JPT][hapmap]
rs4591365	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55894650	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[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];0.96[ASN][1000 genomes]
rs57726945	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57937746	0.91[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	0.81[YRI][hapmap]
rs6546797	1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs6546800	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[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	0.83[JPT][hapmap]
rs6710739	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6710755	0.95[CHB][hapmap];0.81[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6711891	0.81[JPT][hapmap];0.88[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	0.86[JPT][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes]
rs6720817	0.96[ASN][1000 genomes]
rs6727269	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6727919	0.87[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6729266	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs6732369	0.86[JPT][hapmap];0.81[AMR][1000 genomes]
rs6736153	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.99[ASN][1000 genomes]
rs6749237	1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6750069	0.83[JPT][hapmap];0.96[YRI][hapmap]
rs6754779	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6754858	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6757131	0.82[JPT][hapmap]
rs727470	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs727471	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7557173	0.87[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7559074	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7559340	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]
rs7566904	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7570876	0.86[JPT][hapmap];0.93[YRI][hapmap];0.81[AMR][1000 genomes]
rs7579770	0.83[JPT][hapmap]
rs7593322	0.96[ASN][1000 genomes]
rs7597032	0.83[JPT][hapmap]
rs7599657	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7602651	0.81[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs891432	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs891433	0.87[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs893258	0.83[JPT][hapmap]
rs893259	0.81[JPT][hapmap];0.81[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:103 , 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	chr2:73299600-73312600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr2:73299600-73314200	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr2:73299600-73314600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr2:73299600-73314800	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr2:73299600-73315400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr2:73299600-73316000	Weak transcription	NHDF-Ad	bronchial
12	chr2:73299600-73319400	Weak transcription	K562	blood
13	chr2:73299800-73314800	Weak transcription	Brain Substantia Nigra	brain
14	chr2:73299800-73314800	Weak transcription	HSMM	muscle
15	chr2:73300000-73312200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:73300000-73319200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr2:73300200-73314200	Weak transcription	Rectal Smooth Muscle	rectum
18	chr2:73300600-73312600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:73300600-73313000	Strong transcription	Fetal Stomach	stomach
20	chr2:73302600-73312600	Weak transcription	Colon Smooth Muscle	Colon
21	chr2:73302600-73316400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr2:73303000-73328600	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr2:73303200-73320600	Weak transcription	Psoas Muscle	Psoas
24	chr2:73303400-73312600	Weak transcription	Brain Hippocampus Middle	brain
25	chr2:73303400-73313600	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr2:73303400-73320000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr2:73304400-73314200	Weak transcription	HSMMtube	muscle
28	chr2:73305600-73312400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr2:73305600-73313400	Weak transcription	NH-A	brain
30	chr2:73306600-73314800	Weak transcription	HMEC	breast
31	chr2:73307000-73313800	Weak transcription	Left Ventricle	heart
32	chr2:73307200-73314000	Weak transcription	Brain Angular Gyrus	brain
33	chr2:73307400-73314400	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr2:73307800-73313800	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr2:73307800-73314800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr2:73308000-73313600	Weak transcription	Brain Cingulate Gyrus	brain
37	chr2:73308000-73313800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr2:73308400-73312200	Weak transcription	Brain Germinal Matrix	brain
39	chr2:73308400-73312600	Weak transcription	Aorta	Aorta
40	chr2:73308400-73314400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr2:73308600-73312600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr2:73308600-73313400	Weak transcription	Right Ventricle	heart
43	chr2:73308800-73312600	Weak transcription	Brain Anterior Caudate	brain
44	chr2:73308800-73313600	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr2:73309000-73312600	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr2:73309000-73312600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr2:73309000-73314000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr2:73309000-73314200	Weak transcription	Esophagus	oesophagus
49	chr2:73309000-73314400	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr2:73309200-73312600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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