Variant report

Variant	rs2009056
Chromosome Location	chr1:113236230-113236231
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:113163032..113164854-chr1:113235920..113238010,2	K562	blood:
2	chr1:113214782..113217536-chr1:113235013..113236894,2	K562	blood:
3	chr1:113160402..113162739-chr1:113234192..113237024,2	K562	blood:

Variant related genes	Relation type
ENSG00000116489	Chromatin interaction
ENSG00000007341	Chromatin interaction
ENSG00000155363	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10857961	0.82[AFR][1000 genomes]
rs10857967	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1106287	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1110042	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11102501	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11102509	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs11102513	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11102514	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11102520	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11102522	0.87[ASN][1000 genomes]
rs12029985	0.82[AFR][1000 genomes]
rs12030612	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12030641	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12040988	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12049572	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12117479	0.82[AFR][1000 genomes]
rs12120956	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12122980	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12126684	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12126971	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12130243	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12133583	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12140506	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12406282	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12724928	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12728311	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12756815	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17030613	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17030651	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2064711	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2273368	0.82[AFR][1000 genomes]
rs2279499	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2306937	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306940	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2887882	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34107138	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs34569066	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs34848593	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35147679	0.82[AFR][1000 genomes]
rs3737136	0.82[AFR][1000 genomes]
rs3748656	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3795819	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55652172	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs61818802	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61818805	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6679	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs883593	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9308256	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
5	nsv533295	chr1:113167645-113589588	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
6	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
8	nsv529238	chr1:113229946-113759080	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
9	esv997362	chr1:113234820-113243297	Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2009056	ST7L	Cis_1M	lymphoblastoid	RTeQTL
rs2009056	ST7L	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113218600-113240800	Weak transcription	Right Atrium	heart
2	chr1:113219000-113242200	Weak transcription	NHDF-Ad	bronchial
3	chr1:113219000-113243800	Weak transcription	Fetal Brain Male	brain
4	chr1:113222000-113243000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:113228400-113239000	Strong transcription	Fetal Intestine Small	intestine
6	chr1:113228600-113242800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:113228600-113242800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr1:113229000-113242200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr1:113229200-113237200	Weak transcription	Brain Germinal Matrix	brain
10	chr1:113229200-113248000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr1:113229600-113243200	Strong transcription	Dnd41	blood
12	chr1:113230200-113238000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:113230200-113239400	Strong transcription	Fetal Intestine Large	intestine
14	chr1:113230200-113239800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:113230200-113240200	Weak transcription	Fetal Heart	heart
16	chr1:113230200-113240600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:113230200-113240800	Strong transcription	Adipose Nuclei	Adipose
18	chr1:113230200-113241200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:113230200-113242600	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr1:113230200-113243000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:113230200-113243200	Strong transcription	Primary T cells from cord blood	blood
22	chr1:113230400-113240400	Strong transcription	HepG2	liver
23	chr1:113230400-113240600	Strong transcription	Stomach Smooth Muscle	stomach
24	chr1:113230400-113241200	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr1:113230600-113240800	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr1:113230600-113241000	Strong transcription	Gastric	stomach
27	chr1:113230600-113241400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:113230600-113242000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:113230600-113242000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:113230600-113242200	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr1:113230600-113242600	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr1:113230800-113239800	Strong transcription	Liver	Liver
33	chr1:113230800-113240000	Strong transcription	Duodenum Mucosa	Duodenum
34	chr1:113230800-113241400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr1:113231000-113236400	Weak transcription	Brain Angular Gyrus	brain
36	chr1:113231200-113241400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:113231400-113236600	Strong transcription	NHEK	skin
38	chr1:113231400-113241800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr1:113231600-113241200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:113231600-113243000	Weak transcription	Psoas Muscle	Psoas
41	chr1:113231600-113243200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr1:113231800-113237000	Strong transcription	Spleen	Spleen
43	chr1:113231800-113238800	Strong transcription	Placenta Amnion	Placenta Amnion
44	chr1:113231800-113239200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr1:113231800-113239800	Strong transcription	HMEC	breast
46	chr1:113231800-113240000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr1:113231800-113240400	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr1:113231800-113242400	Strong transcription	Osteobl	bone
49	chr1:113231800-113242600	Strong transcription	Fetal Lung	lung
50	chr1:113232000-113240400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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