Variant report

Variant	rs10180995
Chromosome Location	chr2:73310099-73310100
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	POLR2A	chr2:73309981-73311277	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:73306420..73310594-chr2:73310994..73314109,4	K562	blood:
2	chr2:73296621..73300316-chr2:73309682..73312950,4	K562	blood:
3	chr2:73308514..73310297-chr2:73318745..73320278,2	MCF-7	breast:
4	chr2:73308519..73311489-chr2:73401817..73404502,2	K562	blood:

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

Extended variants
information (count: 104 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10166220	0.81[CEU][hapmap];0.95[JPT][hapmap]
rs10167566	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10174548	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10176939	0.81[CEU][hapmap];0.90[JPT][hapmap]
rs10177159	0.86[JPT][hapmap]
rs10180720	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10189744	0.81[CEU][hapmap];0.95[JPT][hapmap]
rs10190861	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10192077	1.00[ASW][hapmap];0.81[CEU][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10197305	0.80[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap]
rs10203608	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1036512	0.81[AMR][1000 genomes]
rs1046186	0.96[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	0.92[ASN][1000 genomes]
rs11885522	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12104691	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12233055	0.81[CEU][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap]
rs12614059	0.89[ASN][1000 genomes]
rs13018842	0.86[ASN][1000 genomes]
rs13385994	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13388404	0.95[JPT][hapmap]
rs13390072	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13391532	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13393567	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13400920	0.94[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13400948	0.88[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.95[ASN][1000 genomes]
rs13403757	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs13403781	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs13407719	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13416407	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]
rs13427947	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1370383	0.82[GIH][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap]
rs1430349	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1430350	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1430351	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17008571	0.90[JPT][hapmap];0.82[YRI][hapmap]
rs17008611	0.82[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap]
rs17008631	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1864488	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.94[ASN][1000 genomes]
rs1992133	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2421098	0.85[CHD][hapmap];0.95[JPT][hapmap]
rs35131031	0.82[ASN][1000 genomes]
rs3813222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.85[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	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]
rs4144837	0.87[CEU][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4514897	0.83[CHD][hapmap];0.95[JPT][hapmap]
rs4591365	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55894650	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55974516	0.83[AMR][1000 genomes]
rs57536428	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57701326	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs57726945	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57937746	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61161134	0.81[AMR][1000 genomes]
rs6546796	0.82[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs6546797	0.88[ASW][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.85[YRI][hapmap]
rs6546800	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6546801	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6709938	0.90[JPT][hapmap]
rs6710739	0.94[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6710755	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.94[ASN][1000 genomes]
rs6711891	0.90[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.83[YRI][hapmap]
rs6712925	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6713655	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6719333	0.81[CEU][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes]
rs6720817	0.96[ASN][1000 genomes]
rs6726940	0.86[JPT][hapmap]
rs6727269	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6727919	0.88[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6729266	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.96[ASN][1000 genomes]
rs6732369	0.80[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap]
rs6736153	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6749237	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6750069	0.81[CEU][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap]
rs6754779	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6754858	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6757131	0.81[CEU][hapmap];0.90[JPT][hapmap]
rs6759733	0.81[CEU][hapmap];0.85[JPT][hapmap];0.81[MEX][hapmap]
rs727470	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs727471	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs732178	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs732179	0.81[CEU][hapmap];0.86[JPT][hapmap]
rs732180	0.81[CEU][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap]
rs7557173	0.83[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7559074	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7559340	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]
rs7566904	0.88[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7570876	0.95[JPT][hapmap]
rs7579770	0.90[JPT][hapmap]
rs7580216	0.81[CEU][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap]
rs7593322	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7597032	0.90[JPT][hapmap]
rs7599657	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7602651	0.94[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs891432	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs891433	0.83[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.96[TSI][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs893258	0.90[JPT][hapmap]
rs893259	0.90[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap]
rs9309471	0.95[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10180995	SFXN5	cis	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

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	chr2:73299800-73311200	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr2:73299800-73314800	Weak transcription	Brain Substantia Nigra	brain
15	chr2:73299800-73314800	Weak transcription	HSMM	muscle
16	chr2:73300000-73312200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:73300000-73319200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr2:73300200-73312000	Weak transcription	Duodenum Mucosa	Duodenum
19	chr2:73300200-73314200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr2:73300400-73310800	Weak transcription	Liver	Liver
21	chr2:73300600-73310400	Strong transcription	Fetal Intestine Small	intestine
22	chr2:73300600-73312600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:73300600-73313000	Strong transcription	Fetal Stomach	stomach
24	chr2:73300800-73311800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr2:73302600-73312600	Weak transcription	Colon Smooth Muscle	Colon
26	chr2:73302600-73316400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr2:73303000-73328600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr2:73303200-73320600	Weak transcription	Psoas Muscle	Psoas
29	chr2:73303400-73312000	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr2:73303400-73312600	Weak transcription	Brain Hippocampus Middle	brain
31	chr2:73303400-73313600	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr2:73303400-73320000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr2:73303600-73311800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr2:73304000-73311800	Weak transcription	Hela-S3	cervix
35	chr2:73304400-73314200	Weak transcription	HSMMtube	muscle
36	chr2:73305000-73311200	Weak transcription	Fetal Kidney	kidney
37	chr2:73305600-73310800	Strong transcription	Colonic Mucosa	Colon
38	chr2:73305600-73312400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr2:73305600-73313400	Weak transcription	NH-A	brain
40	chr2:73306400-73311000	Strong transcription	Gastric	stomach
41	chr2:73306400-73311000	Strong transcription	Stomach Smooth Muscle	stomach
42	chr2:73306600-73314800	Weak transcription	HMEC	breast
43	chr2:73307000-73313800	Weak transcription	Left Ventricle	heart
44	chr2:73307200-73314000	Weak transcription	Brain Angular Gyrus	brain
45	chr2:73307400-73314400	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr2:73307600-73311200	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr2:73307600-73311400	Weak transcription	Osteobl	bone
48	chr2:73307800-73311400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr2:73307800-73311400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr2:73307800-73313800	Weak transcription	Muscle Satellite Cultured Cells	--

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