Variant report

Variant	rs61741479
Chromosome Location	chr1:173915909-173915910
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:173875025..173877652-chr1:173913982..173916465,2	K562	blood:
2	chr1:173835394..173838931-chr1:173914614..173917379,4	MCF-7	breast:
3	chr1:173833863..173839457-chr1:173910408..173918981,14	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234741	Chromatin interaction
ENSG00000185278	Chromatin interaction
ENSG00000208317	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs2227603	0.82[EUR][1000 genomes]
rs74126470	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74126472	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74126473	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74126476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74126478	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74126479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74126480	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74126481	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74126482	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs74126483	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs74126486	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	esv2757761	chr1:173810642-173955943	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
3	esv2758978	chr1:173810642-173955943	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
4	esv3407396	chr1:173896346-173917122	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv916960	chr1:173907804-174080248	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv872550	chr1:173913804-173964206	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv872551	chr1:173913804-174025660	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61741479	RC3H1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173899400-173917400	Strong transcription	Duodenum Smooth Muscle	Duodenum
2	chr1:173899400-173927200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr1:173899400-173929600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:173899600-173923200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:173899800-173953800	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr1:173900000-173929600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr1:173900000-173958600	Strong transcription	Rectal Mucosa Donor 31	rectum
8	chr1:173900000-173962400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:173900000-173966600	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr1:173900000-173968200	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr1:173900200-173966400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:173900400-173964600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:173900800-173963800	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr1:173901200-173931400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:173901400-173962200	Strong transcription	Duodenum Mucosa	Duodenum
16	chr1:173901600-173966400	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr1:173901600-173966400	Strong transcription	Dnd41	blood
18	chr1:173902200-173921200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr1:173902200-173928200	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr1:173902200-173954600	Strong transcription	Primary B cells from peripheral blood	blood
21	chr1:173902600-173954400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr1:173903200-173925000	Strong transcription	Fetal Muscle Trunk	muscle
23	chr1:173903200-173925600	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr1:173903400-173917400	Strong transcription	HUVEC	blood vessel
25	chr1:173903400-173927000	Strong transcription	Fetal Muscle Leg	muscle
26	chr1:173903400-173927000	Strong transcription	Fetal Thymus	thymus
27	chr1:173904000-173929200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:173904000-173966400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:173904800-173921400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr1:173904800-173921400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr1:173904800-173923200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr1:173904800-173954200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr1:173905000-173927000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr1:173905000-173938400	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr1:173905000-173962400	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr1:173905200-173954600	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr1:173906000-173920800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr1:173906000-173925600	Strong transcription	Placenta	Placenta
39	chr1:173906000-173940400	Strong transcription	Adipose Nuclei	Adipose
40	chr1:173906000-173959000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr1:173906200-173920200	Strong transcription	Muscle Satellite Cultured Cells	--
42	chr1:173906200-173920400	Strong transcription	Skeletal Muscle Male	skeletal muscle
43	chr1:173906200-173921400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr1:173906200-173937600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr1:173906400-173931800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:173906800-173918400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr1:173906800-173959000	Strong transcription	Liver	Liver
48	chr1:173907000-173924000	Strong transcription	GM12878-XiMat	blood
49	chr1:173907200-173920200	Strong transcription	Brain Germinal Matrix	brain
50	chr1:173907200-173920600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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