Variant report

Variant	rs12041194
Chromosome Location	chr1:153714252-153714253
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:153712523..153714305-chr1:153717336..153718987,2	K562	blood:
2	chr1:153541303..153542821-chr1:153713408..153715149,2	MCF-7	breast:
3	chr1:153713310..153715419-chr1:153749059..153751923,2	MCF-7	breast:
4	chr1:153712997..153714517-chr1:153747013..153749829,2	MCF-7	breast:
5	chr1:153714105..153716597-chr1:153717786..153720601,2	K562	blood:
6	chr1:153617865..153619831-chr1:153713575..153715568,2	K562	blood:

Variant related genes	Relation type
ENSG00000143554	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11583874	0.86[ASN][1000 genomes]
rs6427268	0.82[ASN][1000 genomes]
rs6698058	0.97[ASN][1000 genomes]
rs7541193	0.82[YRI][hapmap]
rs7545253	0.82[ASN][1000 genomes]
rs7550138	0.85[ASN][1000 genomes]
rs7554642	0.85[ASN][1000 genomes]
rs9426875	0.86[ASN][1000 genomes]
rs9426891	0.99[ASN][1000 genomes]
rs9426902	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv547928	chr1:153612133-153714252	Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv2830411	chr1:153613393-153725007	Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv1067771	chr1:153613593-153724866	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv530052	chr1:153613593-153724866	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
5	nsv1005818	chr1:153613597-153724980	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	nsv535173	chr1:153613597-153724980	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
7	nsv1007835	chr1:153613597-153729959	Genic enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	nsv535174	chr1:153613597-153729959	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
9	nsv1011897	chr1:153613597-153836703	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
10	nsv464028	chr1:153622220-153723037	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
11	nsv547929	chr1:153622220-153723037	Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
12	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
13	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
14	nsv1001312	chr1:153622834-153724867	Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
15	nsv535176	chr1:153622834-153724867	Active TSS Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
16	nsv531892	chr1:153671910-153954090	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
17	nsv1002328	chr1:153672031-153718746	Flanking Active TSS Genic enhancers Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
18	nsv464039	chr1:153708906-153801098	Genic enhancers Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
19	nsv547941	chr1:153708906-153801098	Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs12041194	S100A10	cis	cerebellum	SCAN
rs12041194	S100A10	cis	parietal	SCAN
rs12041194	S100A16	cis	cerebellum	SCAN
rs12041194	S100A13	cis	lymphoblastoid	seeQTL
rs12041194	S100A16	cis	parietal	SCAN
rs12041194	S100A13	cis	parietal	SCAN
rs12041194	SLC27A3	cis	cerebellum	SCAN
rs12041194	S100A2	cis	cerebellum	SCAN
rs12041194	RP1-178F15.4	cis	lung	GTEx
rs12041194	RP1-178F15.4	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153701200-153716200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:153703000-153715800	Weak transcription	Psoas Muscle	Psoas
3	chr1:153703600-153715800	Weak transcription	Fetal Brain Male	brain
4	chr1:153703600-153718200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:153704000-153719600	Weak transcription	Fetal Heart	heart
6	chr1:153706400-153716200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:153707200-153730400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:153707600-153722200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:153708800-153714400	Weak transcription	Stomach Mucosa	stomach
10	chr1:153710000-153714400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:153710000-153716600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:153710400-153714600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:153710400-153714600	Strong transcription	Fetal Intestine Small	intestine
14	chr1:153710600-153714600	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr1:153710800-153715000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:153711400-153714800	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr1:153711400-153718600	Strong transcription	Fetal Stomach	stomach
18	chr1:153711400-153735600	Strong transcription	Fetal Muscle Leg	muscle
19	chr1:153711600-153717000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:153711600-153721400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:153711800-153714400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr1:153712400-153714400	Strong transcription	Fetal Intestine Large	intestine
23	chr1:153712400-153714600	Strong transcription	Ovary	ovary
24	chr1:153712400-153714800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
25	chr1:153712400-153715600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr1:153712400-153719600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr1:153712600-153714800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr1:153712600-153715200	Strong transcription	Fetal Thymus	thymus
29	chr1:153712600-153715800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr1:153712600-153716800	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr1:153712600-153721800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr1:153712600-153721800	Strong transcription	Brain Anterior Caudate	brain
33	chr1:153712600-153722400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:153712600-153741400	Strong transcription	Placenta	Placenta
35	chr1:153712800-153714400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr1:153712800-153714400	Strong transcription	Primary B cells from peripheral blood	blood
37	chr1:153712800-153714400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:153712800-153714600	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr1:153712800-153714600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr1:153712800-153714600	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr1:153712800-153714800	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr1:153712800-153715400	Strong transcription	H9 Cell Line	embryonic stem cell
43	chr1:153712800-153715400	Strong transcription	Brain Angular Gyrus	brain
44	chr1:153712800-153715400	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr1:153712800-153715800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr1:153712800-153716000	Strong transcription	Duodenum Mucosa	Duodenum
47	chr1:153712800-153716600	Strong transcription	NHLF	lung
48	chr1:153712800-153717200	Strong transcription	Brain Substantia Nigra	brain
49	chr1:153712800-153717600	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr1:153712800-153720200	Strong transcription	Skeletal Muscle Female	skeletal muscle

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