Variant report

Variant	rs9842815
Chromosome Location	chr3:105245898-105245899
allele	C/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	FOS	chr3:105245655-105246082	MCF10A-Er-Src	breast:	n/a	chr3:105245953-105245963 chr3:105245953-105245963 chr3:105245953-105245963
2	FOS	chr3:105245781-105246072	MCF10A-Er-Src	breast:	n/a	chr3:105245953-105245963 chr3:105245953-105245963 chr3:105245953-105245963
3	FOS	chr3:105245662-105246095	MCF10A-Er-Src	breast:	n/a	chr3:105245953-105245963 chr3:105245953-105245963 chr3:105245953-105245963
4	POLR2A	chr3:105245469-105245899	H1-neurons	neurons:	n/a	n/a
5	POLR2A	chr3:105245531-105245940	H1-neurons	neurons:	n/a	n/a
6	FOS	chr3:105245775-105246102	MCF10A-Er-Src	breast:	n/a	chr3:105245953-105245963 chr3:105245953-105245963 chr3:105245953-105245963

Variant related genes	Relation type
ALCAM	TF binding region

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1044243	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12632847	0.81[AFR][1000 genomes]
rs13315085	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13315918	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13317140	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13317379	0.82[AMR][1000 genomes]
rs13320956	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13322383	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13325976	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17181561	0.82[AMR][1000 genomes]
rs17181701	0.82[AMR][1000 genomes]
rs17189101	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17189643	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17189711	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2291374	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28452673	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3772552	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72989914	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72989943	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73006164	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7610031	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7619149	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7624777	0.81[AFR][1000 genomes]
rs7633779	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7645474	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9288807	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9288811	0.85[ASN][1000 genomes]
rs9828587	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9829190	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9830049	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9831077	0.82[AMR][1000 genomes]
rs9832489	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9839346	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9840990	0.82[AMR][1000 genomes]
rs9841699	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9842772	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9843750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9847971	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9851399	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9855810	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9859785	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9862725	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9870312	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9873424	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9876895	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9878315	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9990253	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][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	nsv525071	chr3:105004853-105409321	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv829650	chr3:105070893-105255036	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv534224	chr3:105141696-105404293	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv829651	chr3:105203424-105402136	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv460811	chr3:105212993-105316769	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv591240	chr3:105212993-105316769	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105221400-105300400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:105222200-105260600	Weak transcription	Fetal Kidney	kidney
3	chr3:105222800-105246000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:105223800-105274800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:105229600-105260400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr3:105230200-105262600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:105232200-105274000	Weak transcription	HSMMtube	muscle
8	chr3:105233400-105250600	Weak transcription	HSMM	muscle
9	chr3:105234200-105260400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:105234600-105260600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr3:105234600-105261000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:105234600-105274600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr3:105236200-105251000	Weak transcription	Aorta	Aorta
14	chr3:105236400-105251000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr3:105237800-105251000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr3:105237800-105259000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr3:105237800-105274600	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr3:105237800-105275800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr3:105239400-105248000	Weak transcription	HUVEC	blood vessel
20	chr3:105240000-105252400	Weak transcription	Gastric	stomach
21	chr3:105241000-105260400	Weak transcription	Pancreas	Pancrea
22	chr3:105241200-105250600	Enhancers	Pancreatic Islets	Pancreatic Islet
23	chr3:105241600-105250800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr3:105241600-105260200	Weak transcription	HepG2	liver
25	chr3:105241800-105259000	Weak transcription	Primary hematopoietic stem cells	blood
26	chr3:105242000-105259800	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr3:105242000-105293600	Weak transcription	Lung	lung
28	chr3:105242200-105252800	Weak transcription	Fetal Intestine Large	intestine
29	chr3:105242200-105259000	Weak transcription	Ovary	ovary
30	chr3:105242400-105256400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr3:105242400-105280400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr3:105242800-105266800	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr3:105243200-105246400	Strong transcription	GM12878-XiMat	blood
34	chr3:105243200-105248400	Enhancers	Brain Cingulate Gyrus	brain
35	chr3:105243200-105259000	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr3:105244000-105246600	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr3:105244200-105248800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:105244600-105246400	Strong transcription	Liver	Liver
39	chr3:105244600-105252000	Weak transcription	Stomach Smooth Muscle	stomach
40	chr3:105244800-105247600	Enhancers	Osteobl	bone
41	chr3:105244800-105275800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr3:105245000-105246600	Enhancers	Muscle Satellite Cultured Cells	--
43	chr3:105245000-105258800	Weak transcription	Primary B cells from cord blood	blood
44	chr3:105245200-105246000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr3:105245200-105248000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr3:105245200-105250800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:105245200-105259200	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr3:105245400-105246000	Flanking Active TSS	Brain Angular Gyrus	brain
49	chr3:105245400-105246000	Genic enhancers	NHEK	skin
50	chr3:105245400-105246400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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