Variant report

Variant	rs56211824
Chromosome Location	chr1:70815637-70815638
allele	A/G
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	USF1	chr1:70815549-70815673	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:70686767..70689766-chr1:70815216..70817430,2	K562	blood:
2	chr1:70814888..70817395-chr1:70819218..70821847,2	MCF-7	breast:
3	chr1:70814842..70821925-chr1:70874223..70879265,8	K562	blood:
4	chr1:70814864..70817394-chr1:70817734..70820008,3	MCF-7	breast:

Variant related genes	Relation type
HHLA3	TF binding region
ENSG00000116754	Chromatin interaction
ENSG00000197568	Chromatin interaction
ENSG00000118454	Chromatin interaction
ENSG00000116761	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10465863	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11209600	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11209602	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11209603	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11209608	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11209611	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11800138	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12028257	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12029977	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12030275	0.89[AMR][1000 genomes]
rs12031053	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12034101	0.87[AMR][1000 genomes]
rs12036256	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12037272	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12042565	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12565458	0.89[AMR][1000 genomes]
rs12565460	0.87[AMR][1000 genomes]
rs1327873	0.89[AMR][1000 genomes]
rs17131276	0.87[AMR][1000 genomes]
rs17131285	0.87[AMR][1000 genomes]
rs1969953	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4560989	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4650038	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4650041	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4650047	0.89[AMR][1000 genomes]
rs58696538	0.81[AFR][1000 genomes]
rs58997663	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59821213	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60602940	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61122312	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61587863	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61678482	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6686181	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72678630	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72678644	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72678645	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72678646	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72680732	0.87[AMR][1000 genomes]
rs7539544	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs768433	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs998523	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999219	chr1:70730556-71014911	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
2	nsv1012563	chr1:70753332-70832118	Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	esv1792702	chr1:70755511-70818576	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv1801665	chr1:70755511-70832053	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	nsv871430	chr1:70765659-70819912	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv830137	chr1:70765921-70958718	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs56211824	SFRS11	Cis_1M	lymphoblastoid	RTeQTL
rs56211824	HHLA3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70688000-70819200	Weak transcription	Esophagus	oesophagus
2	chr1:70716800-70815800	Weak transcription	Brain Angular Gyrus	brain
3	chr1:70760600-70818200	Weak transcription	Aorta	Aorta
4	chr1:70760600-70818600	Weak transcription	Thymus	Thymus
5	chr1:70762000-70817600	Weak transcription	NHLF	lung
6	chr1:70762200-70818200	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr1:70765600-70818200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr1:70767800-70819000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:70768200-70817000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr1:70770400-70817200	Weak transcription	Pancreas	Pancrea
11	chr1:70773600-70818200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr1:70773800-70818200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr1:70774200-70818000	Weak transcription	Fetal Kidney	kidney
14	chr1:70784200-70817400	Weak transcription	Small Intestine	intestine
15	chr1:70787400-70817600	Weak transcription	Primary hematopoietic stem cells	blood
16	chr1:70788600-70818200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:70789000-70816000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr1:70789200-70818200	Weak transcription	Right Atrium	heart
19	chr1:70790600-70816400	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr1:70790600-70818000	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr1:70790600-70818400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr1:70793600-70818000	Weak transcription	NH-A	brain
23	chr1:70794400-70818000	Weak transcription	HMEC	breast
24	chr1:70797800-70815800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:70798000-70816400	Weak transcription	Brain Anterior Caudate	brain
26	chr1:70799400-70818000	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr1:70799600-70817600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr1:70799600-70818000	Weak transcription	K562	blood
29	chr1:70799600-70818600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr1:70800400-70816400	Weak transcription	Fetal Lung	lung
31	chr1:70800400-70817000	Weak transcription	Adipose Nuclei	Adipose
32	chr1:70800400-70817600	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr1:70800400-70817600	Weak transcription	NHDF-Ad	bronchial
34	chr1:70800400-70818200	Weak transcription	Primary B cells from cord blood	blood
35	chr1:70800400-70818200	Weak transcription	HSMM	muscle
36	chr1:70800400-70818400	Weak transcription	Fetal Intestine Large	intestine
37	chr1:70800400-70819200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr1:70800400-70819200	Weak transcription	Placenta	Placenta
39	chr1:70800600-70817200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr1:70801000-70817600	Weak transcription	Duodenum Mucosa	Duodenum
41	chr1:70801000-70817600	Weak transcription	Left Ventricle	heart
42	chr1:70801400-70816400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr1:70804200-70816400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr1:70804200-70816600	Weak transcription	Primary B cells from peripheral blood	blood
45	chr1:70804800-70818000	Weak transcription	Osteobl	bone
46	chr1:70804800-70818200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr1:70804800-70818200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr1:70804800-70818200	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr1:70805000-70816000	Weak transcription	Primary T cells from cord blood	blood
50	chr1:70805000-70816400	Weak transcription	Primary monocytes fromperipheralblood	blood

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