Variant report

Variant	rs12741973
Chromosome Location	chr1:10638604-10638605
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:10622081..10624385-chr1:10637309..10640742,3	K562	blood:
2	chr1:10632331..10635200-chr1:10638262..10640541,2	K562	blood:
3	chr1:10638213..10640630-chr1:10641912..10644179,2	K562	blood:

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12038548	0.82[CHB][hapmap]
rs2506896	0.91[ASN][1000 genomes]
rs2506901	0.88[CHB][hapmap]
rs2847344	0.84[JPT][hapmap]
rs34575776	0.91[ASN][1000 genomes]
rs4845937	0.82[ASN][1000 genomes]
rs616402	0.88[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap]
rs616488	0.88[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap]
rs6687430	1.00[CEU][hapmap];0.92[GIH][hapmap];0.93[TSI][hapmap];0.89[EUR][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	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1015079	chr1:10611403-10645176	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1009596	chr1:10626249-10652605	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv517464	chr1:10638604-10643197	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv818777	chr1:10638604-10643197	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Optic nerve measurement (rim area)	20395239	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12741973	H6PD	cis	parietal	SCAN
rs12741973	CAMTA1	cis	parietal	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10589400-10664800	Weak transcription	Aorta	Aorta
2	chr1:10591000-10639400	Weak transcription	Hela-S3	cervix
3	chr1:10602000-10639600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:10603000-10659000	Weak transcription	Primary B cells from cord blood	blood
5	chr1:10605000-10659000	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr1:10607600-10641400	Weak transcription	Lung	lung
7	chr1:10623600-10645600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:10624800-10646000	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr1:10627800-10641000	Weak transcription	Fetal Stomach	stomach
10	chr1:10627800-10643000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr1:10628000-10640000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:10628000-10650200	Weak transcription	Fetal Lung	lung
13	chr1:10628400-10661600	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr1:10628800-10651200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr1:10629600-10639000	Weak transcription	Right Ventricle	heart
16	chr1:10629800-10643600	Weak transcription	Fetal Muscle Leg	muscle
17	chr1:10629800-10659000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr1:10630000-10638800	Weak transcription	Primary hematopoietic stem cells	blood
19	chr1:10631800-10659200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr1:10632600-10698000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr1:10635200-10639000	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr1:10635600-10638800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr1:10635600-10639600	Weak transcription	Placenta	Placenta
24	chr1:10635800-10650800	Weak transcription	HSMMtube	muscle
25	chr1:10636000-10639000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:10636000-10639000	Weak transcription	Osteobl	bone
27	chr1:10636000-10650600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr1:10636200-10655600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:10636200-10656000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:10636400-10639000	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr1:10636400-10656200	Weak transcription	NHEK	skin
32	chr1:10636600-10639200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:10636600-10658000	Weak transcription	Spleen	Spleen
34	chr1:10636800-10639000	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr1:10636800-10639400	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr1:10637000-10641600	Weak transcription	Adipose Nuclei	Adipose
37	chr1:10637400-10652200	Weak transcription	Fetal Intestine Small	intestine
38	chr1:10637400-10659000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr1:10637800-10638800	Enhancers	HepG2	liver
40	chr1:10637800-10639200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr1:10637800-10639200	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr1:10638000-10639000	Enhancers	H1 Cell Line	embryonic stem cell
43	chr1:10638000-10639000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr1:10638000-10639000	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr1:10638000-10639000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
46	chr1:10638000-10639000	ZNF genes & repeats	HSMM	muscle
47	chr1:10638000-10639200	Enhancers	H9 Cell Line	embryonic stem cell
48	chr1:10638000-10639400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr1:10638000-10639600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr1:10638000-10640000	Enhancers	HUES48 Cell Line	embryonic stem cell

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