Variant report

Variant	rs61122312
Chromosome Location	chr1:70812707-70812708
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:70812176..70814577-chr1:70818800..70821744,3	MCF-7	breast:
2	chr1:70809714..70814478-chr1:70818976..70822377,5	MCF-7	breast:
3	chr1:70812176..70814908-chr1:70864607..70866509,2	K562	blood:

Variant related genes	Relation type
ENSG00000118454	Chromatin interaction
ENSG00000197568	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];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11209600	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11209602	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11209603	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11209608	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11209611	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11800138	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12028257	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12029977	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12030275	0.88[AMR][1000 genomes]
rs12031053	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12034101	0.86[AMR][1000 genomes]
rs12036256	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12037272	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12042565	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12565458	0.88[AMR][1000 genomes]
rs12565460	0.86[AMR][1000 genomes]
rs1327873	0.88[AMR][1000 genomes]
rs17131276	0.86[AMR][1000 genomes]
rs17131285	0.86[AMR][1000 genomes]
rs1969953	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4560989	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4650038	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4650041	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4650047	0.88[AMR][1000 genomes]
rs56211824	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58696538	0.80[AFR][1000 genomes]
rs58997663	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59821213	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60602940	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61587863	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61678482	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6686181	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72678630	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72678644	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72678645	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72678646	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72680732	0.86[AMR][1000 genomes]
rs7539544	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs768433	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs998523	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[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
rs61122312	SFRS11	Cis_1M	lymphoblastoid	RTeQTL
rs61122312	HHLA3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 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	chr1:70734400-70813000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:70757400-70813200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr1:70760400-70813200	Weak transcription	Fetal Brain Female	brain
6	chr1:70760600-70818200	Weak transcription	Aorta	Aorta
7	chr1:70760600-70818600	Weak transcription	Thymus	Thymus
8	chr1:70762000-70817600	Weak transcription	NHLF	lung
9	chr1:70762200-70818200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr1:70765600-70818200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr1:70767800-70819000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:70768200-70817000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr1:70770400-70817200	Weak transcription	Pancreas	Pancrea
14	chr1:70773600-70818200	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr1:70773800-70818200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr1:70774200-70815200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:70774200-70818000	Weak transcription	Fetal Kidney	kidney
18	chr1:70784200-70813200	Weak transcription	Colon Smooth Muscle	Colon
19	chr1:70784200-70817400	Weak transcription	Small Intestine	intestine
20	chr1:70787400-70817600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr1:70788600-70813200	Weak transcription	GM12878-XiMat	blood
22	chr1:70788600-70818200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:70789000-70813000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr1:70789000-70813200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr1:70789000-70816000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr1:70789200-70818200	Weak transcription	Right Atrium	heart
27	chr1:70790200-70813000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr1:70790600-70813000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr1:70790600-70815400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr1:70790600-70816400	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr1:70790600-70818000	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr1:70790600-70818400	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr1:70793600-70818000	Weak transcription	NH-A	brain
34	chr1:70793800-70813200	Weak transcription	Gastric	stomach
35	chr1:70794400-70818000	Weak transcription	HMEC	breast
36	chr1:70797800-70815800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:70798000-70815000	Weak transcription	NHEK	skin
38	chr1:70798000-70816400	Weak transcription	Brain Anterior Caudate	brain
39	chr1:70799400-70815000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr1:70799400-70818000	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr1:70799600-70817600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr1:70799600-70818000	Weak transcription	K562	blood
43	chr1:70799600-70818600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr1:70800000-70814400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr1:70800400-70814400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:70800400-70815000	Weak transcription	HepG2	liver
47	chr1:70800400-70815200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr1:70800400-70816400	Weak transcription	Fetal Lung	lung
49	chr1:70800400-70817000	Weak transcription	Adipose Nuclei	Adipose
50	chr1:70800400-70817600	Weak transcription	Skeletal Muscle Male	skeletal muscle

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