Variant report

Variant	rs3901273
Chromosome Location	chr2:73316540-73316541
allele	A/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	POLR2A	chr2:73316421-73317109	IMR90	lung:	n/a	n/a
2	JUND	chr2:73316440-73317409	SK-N-SH	brain:	n/a	chr2:73317055-73317066
3	TCF12	chr2:73316465-73317355	SK-N-SH	brain:	n/a	n/a
4	JUND	chr2:73316538-73317296	SK-N-SH	brain:	n/a	chr2:73317055-73317066
5	POLR2A	chr2:73316509-73317255	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:73300909..73302911-chr2:73316133..73317647,2	K562	blood:
2	chr2:73300396..73302911-chr2:73315000..73317633,2	K562	blood:

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

Extended variants
information (count: 100 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10166220	0.82[CEU][hapmap];0.91[JPT][hapmap]
rs10167566	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10174548	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10176939	0.82[CEU][hapmap];0.86[JPT][hapmap]
rs10177159	0.82[JPT][hapmap]
rs10180720	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10180995	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10189744	0.82[CEU][hapmap];0.91[JPT][hapmap]
rs10190861	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10192077	0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10197305	0.86[JPT][hapmap]
rs10203608	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1046186	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10865396	0.86[ASN][1000 genomes]
rs11126389	0.86[ASN][1000 genomes]
rs11686557	0.93[ASN][1000 genomes]
rs11885522	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12104691	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12233055	0.81[JPT][hapmap]
rs12614059	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13018842	0.86[ASN][1000 genomes]
rs13385994	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13388404	0.91[JPT][hapmap]
rs13390072	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13391532	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13393567	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13400920	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13400948	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs13403757	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13403781	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13407719	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13416407	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]
rs13427947	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1430349	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1430350	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1430351	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17008571	0.86[JPT][hapmap]
rs17008611	0.81[JPT][hapmap]
rs17008631	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1864488	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1992133	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap];0.91[AMR][1000 genomes];0.92[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];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3813223	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4144837	0.88[CEU][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4514897	0.90[JPT][hapmap]
rs4591365	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55894650	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55974516	0.82[AMR][1000 genomes]
rs57536428	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57701326	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs57726945	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57937746	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6546796	0.81[JPT][hapmap]
rs6546797	0.81[JPT][hapmap]
rs6546800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6546801	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6709938	0.86[JPT][hapmap]
rs6710739	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6710755	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs6711891	0.86[JPT][hapmap];0.84[YRI][hapmap]
rs6712925	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6713655	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6719333	0.82[CEU][hapmap];0.91[JPT][hapmap]
rs6720817	0.95[ASN][1000 genomes]
rs6726940	0.82[JPT][hapmap]
rs6727269	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6727919	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6729266	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6732369	0.90[JPT][hapmap]
rs6736153	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6749237	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs6750069	0.82[CEU][hapmap];0.86[JPT][hapmap]
rs6754779	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6754858	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6757131	0.82[CEU][hapmap];0.86[JPT][hapmap]
rs6759733	0.80[JPT][hapmap]
rs727470	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs727471	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs732178	0.82[CEU][hapmap]
rs732179	0.82[CEU][hapmap];0.82[JPT][hapmap]
rs7557173	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7559074	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7559340	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]
rs7566904	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7570876	0.91[JPT][hapmap]
rs7579770	0.86[JPT][hapmap]
rs7580216	0.81[JPT][hapmap]
rs7593322	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7597032	0.86[JPT][hapmap]
rs7599657	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7602651	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[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];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs891433	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs893258	0.86[JPT][hapmap]
rs893259	0.86[JPT][hapmap]
rs9309471	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[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:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73299400-73318200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:73299400-73318400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:73299600-73319400	Weak transcription	K562	blood
4	chr2:73300000-73319200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr2:73303000-73328600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr2:73303200-73320600	Weak transcription	Psoas Muscle	Psoas
7	chr2:73303400-73320000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr2:73309200-73319400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr2:73309600-73316600	Strong transcription	HepG2	liver
10	chr2:73312200-73316600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:73313000-73317400	Genic enhancers	Spleen	Spleen
12	chr2:73313000-73319000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr2:73313200-73316600	Strong transcription	Ovary	ovary
14	chr2:73313200-73319000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr2:73313200-73320000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr2:73313200-73327200	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr2:73313400-73316800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr2:73313400-73316800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr2:73313800-73316800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr2:73315200-73317600	Weak transcription	Duodenum Mucosa	Duodenum
21	chr2:73315200-73319000	Enhancers	Fetal Heart	heart
22	chr2:73315400-73318400	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr2:73315400-73319000	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr2:73315600-73316800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr2:73315600-73316800	Active TSS	Aorta	Aorta
26	chr2:73315600-73316800	Genic enhancers	Fetal Intestine Small	intestine
27	chr2:73315600-73318600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:73315600-73319600	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr2:73315600-73330400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr2:73315600-73338000	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr2:73315800-73316600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr2:73315800-73316600	Genic enhancers	NHLF	lung
33	chr2:73315800-73317200	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr2:73315800-73317400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr2:73315800-73317600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr2:73315800-73317800	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr2:73315800-73318200	Weak transcription	Liver	Liver
38	chr2:73315800-73318600	Enhancers	HMEC	breast
39	chr2:73315800-73319000	Weak transcription	Brain Anterior Caudate	brain
40	chr2:73315800-73319800	Weak transcription	Brain Hippocampus Middle	brain
41	chr2:73315800-73320000	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr2:73316000-73317400	Weak transcription	Small Intestine	intestine
43	chr2:73316000-73318400	Weak transcription	Brain Angular Gyrus	brain
44	chr2:73316000-73318400	Weak transcription	Brain Cingulate Gyrus	brain
45	chr2:73316000-73318800	Enhancers	NHDF-Ad	bronchial
46	chr2:73316000-73319600	Enhancers	HSMMtube	muscle
47	chr2:73316000-73320600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr2:73316000-73321000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr2:73316000-73326600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr2:73316200-73316600	Enhancers	Muscle Satellite Cultured Cells	--

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