Variant report

Variant	rs34581400
Chromosome Location	chr9:6472112-6472113
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:6471886-6472290	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr9:6471877-6472307	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:6470925..6472646-chr9:6757849..6760482,2	MCF-7	breast:

Variant related genes	Relation type
C9orf38	TF binding region
ENSG00000107077	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10115294	0.92[EUR][1000 genomes]
rs10119350	0.84[EUR][1000 genomes]
rs10123605	0.92[EUR][1000 genomes]
rs10125313	0.92[EUR][1000 genomes]
rs1037885	0.88[EUR][1000 genomes]
rs10491838	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10739096	0.92[EUR][1000 genomes]
rs10739101	0.96[EUR][1000 genomes]
rs10739103	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10739104	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10758762	0.88[EUR][1000 genomes]
rs10758763	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10758768	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10815400	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10815401	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10815429	0.84[EUR][1000 genomes]
rs10815430	0.92[EUR][1000 genomes]
rs1156869	0.96[EUR][1000 genomes]
rs12346381	0.92[EUR][1000 genomes]
rs1322170	1.00[AMR][1000 genomes]
rs13283464	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs13283631	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs13283687	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13284032	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs13284392	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13285035	0.84[EUR][1000 genomes]
rs13285125	0.88[EUR][1000 genomes]
rs13285152	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13285458	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13285949	0.84[EUR][1000 genomes]
rs13286720	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs13288875	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs13290027	0.84[EUR][1000 genomes]
rs13290126	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs13290488	0.88[EUR][1000 genomes]
rs13291494	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13291887	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs13292030	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs13293015	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13293673	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13294924	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs13296481	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13296692	0.88[EUR][1000 genomes]
rs13298872	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13299896	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13300059	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs13302032	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1381038	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1407357	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1407358	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1563	0.85[AFR][1000 genomes]
rs2019737	0.88[EUR][1000 genomes]
rs2381438	0.80[EUR][1000 genomes]
rs28615746	0.92[EUR][1000 genomes]
rs2890707	0.88[EUR][1000 genomes]
rs34529113	0.84[EUR][1000 genomes]
rs34530211	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34905133	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs35301257	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35408061	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36089474	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3847262	0.88[EUR][1000 genomes]
rs3858051	0.88[EUR][1000 genomes]
rs4008347	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs424119	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4475552	0.80[EUR][1000 genomes]
rs4742177	0.88[EUR][1000 genomes]
rs4742180	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4742198	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4742200	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4742203	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs503315	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs553048	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6477067	0.88[EUR][1000 genomes]
rs67541153	0.88[EUR][1000 genomes]
rs67797327	0.88[EUR][1000 genomes]
rs7021445	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7031407	0.92[EUR][1000 genomes]
rs7031967	0.88[EUR][1000 genomes]
rs7032411	0.93[AMR][1000 genomes]
rs7035574	0.84[EUR][1000 genomes]
rs7036990	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7039968	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7040374	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7043824	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7043887	0.92[EUR][1000 genomes]
rs7044749	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7048431	0.80[EUR][1000 genomes]
rs72693587	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7350177	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7851921	0.92[EUR][1000 genomes]
rs7852138	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7858373	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7859139	0.88[EUR][1000 genomes]
rs7864212	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7869419	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7872349	0.80[EUR][1000 genomes]
rs7873206	0.92[EUR][1000 genomes]
rs7875172	0.84[EUR][1000 genomes]
rs898673	0.88[EUR][1000 genomes]
rs922221	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs993952	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	nsv1029766	chr9:6437020-6523605	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs34581400	C9orf38	Cis_1M	lymphoblastoid	RTeQTL
rs34581400	UHRF2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6414600-6477800	Weak transcription	Placenta	Placenta
2	chr9:6435400-6482000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr9:6438000-6477600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr9:6441600-6475200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr9:6443600-6477600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr9:6450000-6473600	Weak transcription	Small Intestine	intestine
7	chr9:6450000-6477600	Weak transcription	Left Ventricle	heart
8	chr9:6450000-6477600	Weak transcription	HSMMtube	muscle
9	chr9:6450000-6477600	Weak transcription	NHLF	lung
10	chr9:6450000-6478600	Weak transcription	Ovary	ovary
11	chr9:6450000-6482800	Weak transcription	Pancreas	Pancrea
12	chr9:6450200-6477400	Weak transcription	Stomach Smooth Muscle	stomach
13	chr9:6450800-6477400	Weak transcription	Duodenum Mucosa	Duodenum
14	chr9:6451000-6477600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr9:6451200-6475800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr9:6451200-6477600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr9:6452600-6488000	Weak transcription	Colon Smooth Muscle	Colon
18	chr9:6452800-6472200	Weak transcription	Fetal Heart	heart
19	chr9:6452800-6476000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr9:6452800-6481600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr9:6452800-6485400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr9:6452800-6485400	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr9:6456200-6477600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr9:6456200-6477800	Weak transcription	Fetal Brain Female	brain
25	chr9:6458600-6476000	Weak transcription	Fetal Muscle Leg	muscle
26	chr9:6458600-6482800	Weak transcription	Gastric	stomach
27	chr9:6458800-6497200	Weak transcription	Colonic Mucosa	Colon
28	chr9:6459000-6477600	Weak transcription	Fetal Kidney	kidney
29	chr9:6459200-6477600	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr9:6459200-6477800	Weak transcription	Brain Germinal Matrix	brain
31	chr9:6459400-6501800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr9:6460600-6486800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr9:6460800-6475400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr9:6460800-6477600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr9:6461400-6486000	Weak transcription	K562	blood
36	chr9:6462600-6475800	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr9:6462600-6477600	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr9:6463200-6475800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr9:6463400-6475400	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr9:6463600-6518400	Weak transcription	Fetal Brain Male	brain
41	chr9:6463800-6476600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr9:6463800-6477000	Weak transcription	Lung	lung
43	chr9:6464000-6475800	Weak transcription	Adipose Nuclei	Adipose
44	chr9:6464000-6476000	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr9:6465000-6477400	Weak transcription	NH-A	brain
46	chr9:6466200-6472600	Strong transcription	Fetal Thymus	thymus
47	chr9:6466600-6476600	Weak transcription	Fetal Intestine Small	intestine
48	chr9:6466800-6476600	Weak transcription	Fetal Stomach	stomach
49	chr9:6467200-6475800	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr9:6467400-6473000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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