Variant report

Variant	rs7044749
Chromosome Location	chr9:6415241-6415242
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:6413231..6415998-chr9:6419721..6423966,4	MCF-7	breast:
2	chr9:6411739..6415458-chr9:6420668..6426596,8	K562	blood:
3	chr9:6412168..6415418-chr9:6418500..6425043,7	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C9orf38-1	chr9:6415145-6415563	ENSG00000233367.1

Variant related genes	Relation type
ENSG00000147854	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10115294	0.96[EUR][1000 genomes]
rs10123605	0.96[EUR][1000 genomes]
rs10125313	0.96[EUR][1000 genomes]
rs1037885	0.91[EUR][1000 genomes]
rs1048279	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10491838	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10739096	0.96[EUR][1000 genomes]
rs10739101	1.00[EUR][1000 genomes]
rs10739103	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10739104	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10758762	0.91[EUR][1000 genomes]
rs10758763	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10758768	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10815400	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10815401	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10815429	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs10815430	0.96[EUR][1000 genomes]
rs1156869	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12346381	0.88[EUR][1000 genomes]
rs1322170	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13283464	0.83[EUR][1000 genomes]
rs13283631	0.83[EUR][1000 genomes]
rs13283687	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13284392	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13285125	0.83[EUR][1000 genomes]
rs13285152	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13285458	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13288875	0.83[EUR][1000 genomes]
rs13290488	0.83[EUR][1000 genomes]
rs13291494	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13291887	0.83[EUR][1000 genomes]
rs13293015	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13293673	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13294924	0.83[EUR][1000 genomes]
rs13296481	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13296692	0.83[EUR][1000 genomes]
rs13298872	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13299896	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13300059	0.83[EUR][1000 genomes]
rs13302032	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1330381	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1381038	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1407357	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1407358	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1412420	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1854709	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1855022	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2000198	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2019737	0.91[EUR][1000 genomes]
rs2051003	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2150964	0.81[EUR][1000 genomes]
rs2150971	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2381438	0.84[EUR][1000 genomes]
rs28615746	0.96[EUR][1000 genomes]
rs2890707	0.91[EUR][1000 genomes]
rs34530211	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34581400	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35301257	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35408061	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36089474	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3847262	0.91[EUR][1000 genomes]
rs3858051	0.91[EUR][1000 genomes]
rs4008347	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs424119	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4475552	0.84[EUR][1000 genomes]
rs4742172	0.96[EUR][1000 genomes]
rs4742177	0.91[EUR][1000 genomes]
rs4742180	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4742198	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742200	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742203	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs503315	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs553048	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6477060	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6477067	0.91[EUR][1000 genomes]
rs67541153	0.91[EUR][1000 genomes]
rs67797327	0.83[EUR][1000 genomes]
rs7021445	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7031407	0.96[EUR][1000 genomes]
rs7031967	0.92[EUR][1000 genomes]
rs7032411	0.93[AMR][1000 genomes]
rs7035574	0.88[EUR][1000 genomes]
rs7036990	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7039968	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7040374	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7043824	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7043887	0.96[EUR][1000 genomes]
rs7048431	0.84[EUR][1000 genomes]
rs72693587	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7350177	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7851921	0.85[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs7852138	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7853322	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7858373	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7859139	0.91[EUR][1000 genomes]
rs7864212	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7869419	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7873206	0.96[EUR][1000 genomes]
rs898673	0.91[EUR][1000 genomes]
rs922221	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs980849	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs980850	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs993952	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948847	chr9:5712626-6417677	Strong transcription Enhancers Weak transcription Flanking Active TSS 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 miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv933124	chr9:6099101-6644738	Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv1029000	chr9:6188652-6687205	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
6	nsv1031459	chr9:6216913-6657192	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv948562	chr9:6222553-6684955	Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
8	nsv1032350	chr9:6328167-6630686	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv892160	chr9:6364449-6506038	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv892161	chr9:6364449-6523056	Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats 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	19 gene(s)	inside rSNPs	diseases
11	nsv831497	chr9:6377501-6612402	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
12	esv3440128	chr9:6412477-6415325	Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7044749	C9orf38	Cis_1M	lymphoblastoid	RTeQTL
rs7044749	UHRF2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6411800-6415600	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr9:6412200-6415400	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr9:6412200-6415400	Active TSS	Fetal Intestine Large	intestine
4	chr9:6412200-6415400	Active TSS	Ovary	ovary
5	chr9:6412200-6415400	Active TSS	Psoas Muscle	Psoas
6	chr9:6412200-6415800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr9:6412400-6415400	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr9:6412400-6415400	Active TSS	HSMMtube	muscle
9	chr9:6412600-6415400	Active TSS	NHLF	lung
10	chr9:6412800-6415400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr9:6412800-6415400	Active TSS	Muscle Satellite Cultured Cells	--
12	chr9:6412800-6415400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr9:6412800-6415800	Active TSS	HMEC	breast
14	chr9:6413400-6415600	Flanking Active TSS	Primary hematopoietic stem cells	blood
15	chr9:6413600-6415600	Flanking Active TSS	Primary B cells from cord blood	blood
16	chr9:6414000-6415400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr9:6414000-6415400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr9:6414000-6415600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr9:6414200-6415600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr9:6414200-6415600	Flanking Active TSS	Duodenum Mucosa	Duodenum
21	chr9:6414200-6415800	Flanking Active TSS	Primary T cells from cord blood	blood
22	chr9:6414200-6415800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr9:6414200-6415800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr9:6414200-6416000	Transcr. at gene 5' and 3'	Dnd41	blood
25	chr9:6414400-6415400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
26	chr9:6414400-6415400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
27	chr9:6414400-6415400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
28	chr9:6414400-6415400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr9:6414400-6415400	Flanking Active TSS	Brain Anterior Caudate	brain
30	chr9:6414400-6415600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
31	chr9:6414400-6415600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
32	chr9:6414400-6415600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr9:6414400-6415600	Flanking Active TSS	Fetal Brain Male	brain
34	chr9:6414400-6415600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr9:6414400-6416400	Enhancers	Spleen	Spleen
36	chr9:6414400-6427400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr9:6414600-6415400	Flanking Active TSS	Fetal Heart	heart
38	chr9:6414600-6415400	Weak transcription	Lung	lung
39	chr9:6414600-6415600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
40	chr9:6414600-6415600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr9:6414600-6415600	Enhancers	Primary neutrophils fromperipheralblood	blood
42	chr9:6414600-6415600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr9:6414600-6415600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr9:6414600-6415600	Flanking Active TSS	Brain Germinal Matrix	brain
45	chr9:6414600-6415600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
46	chr9:6414600-6416000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr9:6414600-6416000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr9:6414600-6416000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr9:6414600-6416000	Enhancers	Placenta Amnion	Placenta Amnion
50	chr9:6414600-6416000	Flanking Active TSS	Osteobl	bone

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