Variant report

Variant	rs575662
Chromosome Location	chr11:77072290-77072291
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	SP1	chr11:77072267-77072558	H1-hESC	embryonic stem cell:	n/a	n/a
2	TCF12	chr11:77072205-77072605	H1-hESC	embryonic stem cell:	n/a	n/a
3	TEAD4	chr11:77072254-77072625	H1-hESC	embryonic stem cell:	n/a	n/a
4	TEAD4	chr11:77072119-77072654	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr11:77072251-77072502	SK-N-SH	brain:	n/a	n/a
6	TEAD4	chr11:77072176-77072692	H1-hESC	embryonic stem cell:	n/a	n/a
7	TEAD4	chr11:77072193-77072594	ECC-1	luminal epithelium:	n/a	n/a
8	EP300	chr11:77072193-77072612	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
PAK1	TF binding region

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10793248	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10899379	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs11600983	0.81[EUR][1000 genomes]
rs11607378	0.85[EUR][1000 genomes]
rs1225479	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1670459	0.91[JPT][hapmap]
rs1793476	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs1793483	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs1901821	0.82[CEU][hapmap]
rs2007466	0.84[EUR][1000 genomes]
rs2602463	0.81[ASN][1000 genomes]
rs2602465	0.95[JPT][hapmap]
rs2602472	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2725812	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2729747	0.81[ASN][1000 genomes]
rs2729753	0.81[ASN][1000 genomes]
rs2729762	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs2729771	0.81[ASN][1000 genomes]
rs2844333	0.95[JPT][hapmap]
rs2853097	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3015984	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3015989	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3015991	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3015993	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3019240	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3019243	0.82[EUR][1000 genomes]
rs3019258	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34420077	0.86[EUR][1000 genomes]
rs4433591	0.86[EUR][1000 genomes]
rs473012	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs476258	0.80[AFR][1000 genomes]
rs476925	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs478134	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs478475	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs482243	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs487322	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs489038	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs491781	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs492527	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4944153	0.80[EUR][1000 genomes]
rs4944155	0.85[EUR][1000 genomes]
rs4944158	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4945162	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs4945166	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes]
rs4945169	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs495889	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs497172	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs497946	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs499880	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs500731	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs514191	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs517511	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs538670	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs539906	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs556696	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs561153	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs562939	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs568309	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57129983	0.85[EUR][1000 genomes]
rs576079	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs576997	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs584909	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs599437	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs605910	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs614775	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs618012	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61901769	0.85[EUR][1000 genomes]
rs61901771	0.82[EUR][1000 genomes]
rs61901802	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs628325	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs635291	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs639857	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6592714	0.81[EUR][1000 genomes]
rs6592715	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs667331	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs674652	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap]
rs683497	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs688212	0.95[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7118869	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs721382	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs73496890	0.83[EUR][1000 genomes]
rs7928731	0.85[EUR][1000 genomes]
rs883223	0.86[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap]
rs98703	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048360	chr11:76900813-77387933	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv541089	chr11:76900813-77387933	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1049603	chr11:76900813-77520411	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv541090	chr11:76900813-77520411	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv3424135	chr11:76961603-77277087	Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1037724	chr11:77061945-77250391	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv541091	chr11:77061945-77250391	Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77030600-77086800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr11:77031600-77073800	Weak transcription	Spleen	Spleen
3	chr11:77033400-77090400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr11:77034400-77086200	Weak transcription	NHLF	lung
5	chr11:77042800-77080800	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr11:77043400-77072600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:77043400-77074800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr11:77043400-77082400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr11:77043400-77083600	Weak transcription	Thymus	Thymus
10	chr11:77043800-77088400	Weak transcription	Colonic Mucosa	Colon
11	chr11:77044200-77075000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr11:77046200-77077000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr11:77046200-77092400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr11:77046800-77121600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr11:77047200-77096000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr11:77047400-77089000	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr11:77047400-77090000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr11:77047800-77075000	Weak transcription	Left Ventricle	heart
19	chr11:77047800-77075600	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr11:77048600-77087800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr11:77052600-77085600	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr11:77055000-77085000	Weak transcription	Primary B cells from peripheral blood	blood
23	chr11:77055200-77083400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr11:77055200-77092200	Weak transcription	Small Intestine	intestine
25	chr11:77055200-77117600	Weak transcription	Pancreas	Pancrea
26	chr11:77057400-77088000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr11:77058600-77075000	Weak transcription	NH-A	brain
28	chr11:77059800-77085800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr11:77059800-77088800	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr11:77060400-77084000	Weak transcription	Fetal Stomach	stomach
31	chr11:77063200-77081000	Weak transcription	Stomach Mucosa	stomach
32	chr11:77064200-77102800	Weak transcription	Brain Substantia Nigra	brain
33	chr11:77064600-77083000	Weak transcription	Brain Anterior Caudate	brain
34	chr11:77064600-77085400	Weak transcription	Brain Hippocampus Middle	brain
35	chr11:77064800-77076600	Weak transcription	Fetal Thymus	thymus
36	chr11:77064800-77085200	Weak transcription	Osteobl	bone
37	chr11:77066000-77084000	Weak transcription	Colon Smooth Muscle	Colon
38	chr11:77066800-77090000	Weak transcription	Brain Angular Gyrus	brain
39	chr11:77067000-77076600	Weak transcription	Fetal Intestine Small	intestine
40	chr11:77067000-77085600	Weak transcription	A549	lung
41	chr11:77067000-77088000	Weak transcription	Gastric	stomach
42	chr11:77067000-77088200	Weak transcription	Liver	Liver
43	chr11:77067000-77092800	Weak transcription	Rectal Smooth Muscle	rectum
44	chr11:77067000-77093800	Weak transcription	Psoas Muscle	Psoas
45	chr11:77067000-77097000	Weak transcription	Esophagus	oesophagus
46	chr11:77067200-77111800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr11:77067600-77083000	Weak transcription	Fetal Kidney	kidney
48	chr11:77068400-77083400	Weak transcription	Aorta	Aorta
49	chr11:77068600-77085600	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr11:77068600-77085800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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