Variant report

Variant	rs12040988
Chromosome Location	chr1:113173804-113173805
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:113172398..113173913-chr1:113190499..113193420,2	K562	blood:
2	chr1:112902471..112904026-chr1:113171966..113173956,2	K562	blood:
3	chr1:113160723..113165186-chr1:113170921..113177730,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000007341	Chromatin interaction
ENSG00000231246	Chromatin interaction
ENSG00000116489	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10857961	0.87[AFR][1000 genomes]
rs10857964	0.82[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs10857967	0.82[CHB][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1106287	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1110042	0.88[EUR][1000 genomes]
rs11102496	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11102498	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11102501	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11102509	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11102513	0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11102514	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11102520	0.88[EUR][1000 genomes]
rs11102522	0.95[JPT][hapmap];0.82[YRI][hapmap]
rs12029985	0.87[AFR][1000 genomes]
rs12030612	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12030641	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12045227	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12049572	0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12117479	0.87[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12120956	0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12122980	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12126684	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12126971	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12130243	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133583	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12137269	0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12140506	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12406282	0.88[EUR][1000 genomes]
rs12406530	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12724928	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12728311	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12756815	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17030613	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17030651	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2009056	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2064711	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2273368	0.81[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2279499	0.83[ASN][1000 genomes]
rs2306937	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2306940	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2887882	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34107138	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34569066	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34848593	0.88[EUR][1000 genomes]
rs35147679	0.87[AFR][1000 genomes]
rs3737136	0.82[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs3748656	0.88[EUR][1000 genomes]
rs3795819	0.88[EUR][1000 genomes]
rs55652172	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56135413	0.80[EUR][1000 genomes]
rs60900293	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs61818802	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61818805	0.88[EUR][1000 genomes]
rs6679	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7522283	0.95[JPT][hapmap]
rs883593	0.88[EUR][1000 genomes]
rs9308256	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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	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	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
5	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
6	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12040988	ST7L	cis	multi-tissue	Pritchard
rs12040988	ST7L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113163600-113180600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:113163600-113200000	Weak transcription	Fetal Kidney	kidney
3	chr1:113163800-113176000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr1:113163800-113200200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr1:113163800-113200800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:113164000-113190000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr1:113164200-113175800	Weak transcription	Fetal Brain Female	brain
8	chr1:113164200-113180000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:113164200-113204200	Weak transcription	Fetal Brain Male	brain
10	chr1:113164800-113179200	Weak transcription	Colonic Mucosa	Colon
11	chr1:113165400-113174400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:113165400-113175200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr1:113165400-113176400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:113165600-113174400	Genic enhancers	K562	blood
15	chr1:113167800-113176200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr1:113168000-113180000	Weak transcription	Aorta	Aorta
17	chr1:113168600-113177800	Weak transcription	Fetal Intestine Large	intestine
18	chr1:113168600-113179200	Weak transcription	NH-A	brain
19	chr1:113168800-113174000	Weak transcription	Psoas Muscle	Psoas
20	chr1:113168800-113174800	Weak transcription	Right Atrium	heart
21	chr1:113168800-113177600	Weak transcription	Stomach Mucosa	stomach
22	chr1:113168800-113177800	Weak transcription	NHLF	lung
23	chr1:113168800-113178200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:113168800-113179200	Weak transcription	Brain Angular Gyrus	brain
25	chr1:113168800-113179200	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr1:113168800-113179200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr1:113168800-113179400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr1:113168800-113180000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:113168800-113180000	Weak transcription	Lung	lung
30	chr1:113168800-113187200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr1:113168800-113189800	Weak transcription	Fetal Lung	lung
32	chr1:113168800-113191000	Weak transcription	Ovary	ovary
33	chr1:113168800-113199800	Weak transcription	Esophagus	oesophagus
34	chr1:113168800-113215800	Weak transcription	Fetal Heart	heart
35	chr1:113169000-113181600	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr1:113169000-113186400	Weak transcription	Fetal Muscle Trunk	muscle
37	chr1:113169000-113189800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:113169200-113174800	Weak transcription	Gastric	stomach
39	chr1:113169200-113188400	Weak transcription	Left Ventricle	heart
40	chr1:113169800-113176600	Weak transcription	A549	lung
41	chr1:113169800-113178600	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr1:113169800-113188800	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr1:113170000-113174800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr1:113170000-113179200	Weak transcription	Duodenum Mucosa	Duodenum
45	chr1:113171200-113174000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr1:113171200-113175000	Strong transcription	Primary T cells from cord blood	blood
47	chr1:113171400-113174800	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr1:113171400-113175800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:113171400-113176200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
50	chr1:113171600-113174000	Strong transcription	NHDF-Ad	bronchial

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