Variant report

Variant	rs11102498
Chromosome Location	chr1:113119442-113119443
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:113117690..113119530-chr1:113159900..113161973,2	K562	blood:

Variant related genes	Relation type
ENSG00000116489	Chromatin interaction
ENSG00000007341	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10857961	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10857964	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10857967	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11102496	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11102501	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11102509	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11102513	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11102514	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12029985	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12030612	0.81[ASN][1000 genomes]
rs12030641	0.81[ASN][1000 genomes]
rs12040988	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12045227	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12049572	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12117479	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12120956	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12122980	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12130243	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12137269	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12140506	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12406530	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12724928	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12728311	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12756815	0.81[ASN][1000 genomes]
rs17030613	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2064711	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2887882	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34107138	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34199214	0.84[EUR][1000 genomes]
rs34569066	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35023236	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35147679	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3737136	0.82[EUR][1000 genomes]
rs55652172	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56135413	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60900293	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61818802	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9308256	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv13370	chr1:112693290-113246263	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
4	nsv831081	chr1:112934920-113122640	Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv432631	chr1:113071834-113200797	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11102498	ST7L	Cis_1M	lymphoblastoid	RTeQTL
rs11102498	ST7L	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113060200-113132400	Weak transcription	Pancreas	Pancrea
2	chr1:113064400-113132200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr1:113066000-113132200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr1:113070400-113120600	Weak transcription	Right Ventricle	heart
5	chr1:113070600-113120200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr1:113070600-113132400	Weak transcription	Aorta	Aorta
7	chr1:113081200-113132200	Weak transcription	Primary B cells from cord blood	blood
8	chr1:113081400-113132400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr1:113081800-113132200	Weak transcription	Primary B cells from peripheral blood	blood
10	chr1:113083200-113123200	Weak transcription	Right Atrium	heart
11	chr1:113084000-113131400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:113084600-113120600	Weak transcription	Ovary	ovary
13	chr1:113084800-113137000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr1:113087600-113125800	Weak transcription	Colon Smooth Muscle	Colon
15	chr1:113088400-113132200	Weak transcription	HMEC	breast
16	chr1:113089800-113120400	Weak transcription	Stomach Mucosa	stomach
17	chr1:113092000-113151200	Weak transcription	Colonic Mucosa	Colon
18	chr1:113100600-113120400	Weak transcription	Fetal Heart	heart
19	chr1:113100600-113120400	Weak transcription	NHLF	lung
20	chr1:113105400-113129800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:113109000-113123000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr1:113109000-113160000	Weak transcription	Gastric	stomach
23	chr1:113109200-113152600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:113109400-113122400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr1:113111000-113131000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr1:113111800-113138800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr1:113112000-113128200	Strong transcription	Liver	Liver
28	chr1:113112200-113120400	Weak transcription	Fetal Kidney	kidney
29	chr1:113112600-113131800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr1:113113200-113124400	Strong transcription	Fetal Muscle Trunk	muscle
31	chr1:113113200-113132400	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr1:113113800-113119800	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr1:113113800-113124400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:113114200-113121800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr1:113114400-113121200	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr1:113114400-113124600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:113114600-113119600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:113114600-113122000	Strong transcription	Fetal Muscle Leg	muscle
39	chr1:113114800-113121800	Strong transcription	Stomach Smooth Muscle	stomach
40	chr1:113115000-113120600	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr1:113115000-113128800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr1:113115200-113120600	Weak transcription	Brain Anterior Caudate	brain
43	chr1:113115200-113123800	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr1:113115200-113130200	Weak transcription	Brain Cingulate Gyrus	brain
45	chr1:113115400-113123800	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr1:113115400-113154200	Weak transcription	Esophagus	oesophagus
47	chr1:113115800-113120400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:113115800-113130800	Weak transcription	Fetal Brain Male	brain
49	chr1:113115800-113160000	Weak transcription	Small Intestine	intestine
50	chr1:113116000-113132400	Weak transcription	Thymus	Thymus

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