Variant report

Variant	rs11101377
Chromosome Location	chr10:49745229-49745230
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:49744902..49747095-chr10:49766693..49768788,2	K562	blood:
2	chr10:49744876..49747052-chr10:49752993..49755068,2	K562	blood:
3	chr10:49725693..49727830-chr10:49743883..49745489,2	K562	blood:
4	chr10:49713932..49717816-chr10:49742746..49746059,3	K562	blood:
5	chr10:49744884..49749313-chr10:49750312..49755068,6	K562	blood:
6	chr10:49740700..49743392-chr10:49743938..49745981,2	K562	blood:

Variant related genes	Relation type
ENSG00000231906	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10491040	0.85[ASN][1000 genomes]
rs10735226	1.00[JPT][hapmap]
rs10776614	0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10776615	0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10776616	0.82[CHB][hapmap];0.91[ASN][1000 genomes]
rs10857592	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10857596	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10857598	0.85[ASN][1000 genomes]
rs11101355	1.00[JPT][hapmap]
rs11101357	1.00[JPT][hapmap]
rs11101362	0.81[ASN][1000 genomes]
rs11101364	0.81[ASN][1000 genomes]
rs11101368	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11101381	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11101382	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11101384	0.82[CHB][hapmap];0.93[ASN][1000 genomes]
rs11591281	0.81[ASN][1000 genomes]
rs11812546	1.00[JPT][hapmap]
rs12358311	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12358315	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12412164	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12777174	1.00[JPT][hapmap]
rs12777190	1.00[JPT][hapmap]
rs1345104	0.82[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.93[ASN][1000 genomes]
rs1345109	0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1345110	0.92[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1345111	0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1348633	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1445148	0.89[ASN][1000 genomes]
rs1473323	0.81[ASN][1000 genomes]
rs17697885	1.00[JPT][hapmap]
rs17770615	1.00[JPT][hapmap]
rs1814469	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1838568	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1838569	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1838570	0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1838573	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1838574	0.85[ASN][1000 genomes]
rs1838579	0.82[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.93[ASN][1000 genomes]
rs1900021	0.87[ASN][1000 genomes]
rs1965170	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2077152	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2120910	0.82[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.93[ASN][1000 genomes]
rs34983450	0.81[ASN][1000 genomes]
rs4080665	1.00[JPT][hapmap]
rs4084916	0.85[ASN][1000 genomes]
rs4101278	0.87[ASN][1000 genomes]
rs41510345	1.00[JPT][hapmap]
rs4450130	1.00[JPT][hapmap];0.80[MEX][hapmap];0.81[ASN][1000 genomes]
rs4838418	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4838421	0.93[ASN][1000 genomes]
rs4838422	0.93[ASN][1000 genomes]
rs4838605	1.00[JPT][hapmap]
rs4838606	1.00[JPT][hapmap]
rs4838617	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4838623	0.82[CHB][hapmap];0.93[ASN][1000 genomes]
rs56058334	0.89[ASN][1000 genomes]
rs56080723	0.87[ASN][1000 genomes]
rs56248718	0.87[ASN][1000 genomes]
rs57601353	0.81[ASN][1000 genomes]
rs6537568	0.88[ASN][1000 genomes]
rs66695288	0.81[ASN][1000 genomes]
rs67372461	0.81[ASN][1000 genomes]
rs7069220	1.00[JPT][hapmap]
rs7071095	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7071480	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7072237	0.88[ASN][1000 genomes]
rs7074631	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7085183	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7085335	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7087729	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7088010	0.89[ASN][1000 genomes]
rs7093726	1.00[JPT][hapmap]
rs7094216	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7096053	0.95[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7098068	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7350424	0.89[ASN][1000 genomes]
rs7350439	0.89[ASN][1000 genomes]
rs747533	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7894707	0.82[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.89[ASN][1000 genomes]
rs7894971	0.82[CHB][hapmap];0.93[ASN][1000 genomes]
rs7896644	0.82[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.93[ASN][1000 genomes]
rs7904456	0.89[ASN][1000 genomes]
rs7905247	0.82[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.93[ASN][1000 genomes]
rs7911247	1.00[JPT][hapmap]
rs7915233	1.00[JPT][hapmap]
rs7916108	0.82[CHB][hapmap];0.93[ASN][1000 genomes]
rs935271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[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	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv895372	chr10:49576878-49933488	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11101377	A1CF	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49732200-49750800	Weak transcription	Gastric	stomach
2	chr10:49734400-49762400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr10:49735400-49749400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr10:49735400-49756800	Weak transcription	HSMMtube	muscle
5	chr10:49735600-49755600	Weak transcription	Brain Angular Gyrus	brain
6	chr10:49736200-49749400	Weak transcription	HUVEC	blood vessel
7	chr10:49739400-49762400	Weak transcription	Stomach Smooth Muscle	stomach
8	chr10:49740800-49746200	Strong transcription	NHLF	lung
9	chr10:49741000-49747000	Strong transcription	Muscle Satellite Cultured Cells	--
10	chr10:49741600-49746400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr10:49741600-49746600	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr10:49741600-49746600	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr10:49741600-49746600	Strong transcription	Osteobl	bone
14	chr10:49741800-49746400	Enhancers	H1 Cell Line	embryonic stem cell
15	chr10:49742000-49745400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr10:49742000-49746400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr10:49742200-49747200	Strong transcription	HSMM	muscle
18	chr10:49742600-49749000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr10:49742600-49774800	Weak transcription	Aorta	Aorta
20	chr10:49742800-49746400	Strong transcription	NHDF-Ad	bronchial
21	chr10:49742800-49747200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr10:49742800-49755200	Weak transcription	Brain Cingulate Gyrus	brain
23	chr10:49742800-49755200	Weak transcription	Brain Hippocampus Middle	brain
24	chr10:49742800-49755600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr10:49743400-49746400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr10:49743600-49746400	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr10:49743800-49757800	Weak transcription	HMEC	breast
28	chr10:49744000-49745800	Weak transcription	Brain Substantia Nigra	brain
29	chr10:49744200-49745400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr10:49744200-49746400	Enhancers	H9 Cell Line	embryonic stem cell
31	chr10:49744200-49746400	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr10:49744400-49745600	Enhancers	Fetal Lung	lung
33	chr10:49744600-49745600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr10:49744600-49745600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr10:49744600-49746000	Strong transcription	NH-A	brain
36	chr10:49744800-49745400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr10:49744800-49745600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
38	chr10:49744800-49746400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr10:49745200-49745400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr10:49745200-49745600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
41	chr10:49745200-49745600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
42	chr10:49745200-49748800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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