Variant report

Variant	rs4670269
Chromosome Location	chr2:39198036-39198037
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39197261..39199568-chr2:39199953..39202278,2	MCF-7	breast:
2	chr2:39192683..39195267-chr2:39196108..39199516,3	K562	blood:
3	chr2:39155848..39158536-chr2:39196585..39199422,2	K562	blood:
4	chr2:39196307..39199033-chr2:39213490..39215469,3	K562	blood:
5	chr2:39186143..39188082-chr2:39196779..39198983,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000214694	Chromatin interaction
ENSG00000269210	Chromatin interaction
ENSG00000115904	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10165968	0.88[CEU][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap]
rs10166395	0.88[CEU][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10166801	0.87[CEU][hapmap];0.83[CHB][hapmap]
rs10172714	0.87[CEU][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap];0.93[EUR][1000 genomes]
rs10177250	0.88[CEU][hapmap];0.92[CHB][hapmap]
rs10183915	0.82[CHB][hapmap];0.84[EUR][1000 genomes]
rs10186762	0.87[CEU][hapmap];0.83[CHB][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10190377	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs10192250	0.87[CEU][hapmap];0.92[CHB][hapmap];0.82[EUR][1000 genomes]
rs10194374	0.87[CEU][hapmap];0.83[CHB][hapmap]
rs10201980	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs10206751	0.88[JPT][hapmap]
rs1037495	0.88[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1043793	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10779924	0.93[EUR][1000 genomes]
rs12471731	0.88[CEU][hapmap];0.92[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap]
rs12620003	0.82[CEU][hapmap]
rs12622969	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs12712630	0.83[CHB][hapmap]
rs13023273	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13031871	0.84[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap]
rs1377860	0.87[CEU][hapmap];0.81[CHB][hapmap];1.00[TSI][hapmap]
rs1377864	0.88[CEU][hapmap]
rs1454221	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1454222	0.87[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1454223	0.87[CEU][hapmap];0.92[CHB][hapmap];0.84[CHD][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1454225	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1454226	0.87[CEU][hapmap];0.83[CHB][hapmap]
rs1470914	0.88[CEU][hapmap]
rs1470915	0.87[CEU][hapmap];0.83[CHB][hapmap];0.86[GIH][hapmap];1.00[TSI][hapmap]
rs1531021	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1869513	0.87[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs1869514	0.93[EUR][1000 genomes]
rs1947432	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2060987	0.93[TSI][hapmap]
rs2060988	0.83[GIH][hapmap]
rs2123876	0.87[CEU][hapmap]
rs2123879	0.82[CHB][hapmap]
rs2123881	0.87[CEU][hapmap];0.83[CHB][hapmap]
rs2168042	0.92[CHB][hapmap]
rs2168044	0.93[EUR][1000 genomes]
rs2278912	0.93[EUR][1000 genomes]
rs2278913	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2278914	0.87[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2290445	0.87[CEU][hapmap];0.92[CHB][hapmap];0.81[CHD][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2305516	0.87[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2373495	0.87[CEU][hapmap];0.83[CHB][hapmap]
rs2373496	0.87[CEU][hapmap];0.81[CHB][hapmap]
rs2373497	0.81[CHD][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap]
rs2888585	0.87[CEU][hapmap];0.92[CHB][hapmap]
rs297120	0.88[CEU][hapmap];0.81[CHD][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap]
rs297124	0.88[CEU][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap]
rs297134	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs297135	0.87[CEU][hapmap];0.92[CHB][hapmap]
rs297136	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs297142	0.88[CEU][hapmap];0.90[GIH][hapmap]
rs297144	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs297148	1.00[CHB][hapmap]
rs297149	0.86[CEU][hapmap];0.92[CHB][hapmap]
rs297150	0.87[CEU][hapmap];0.92[CHB][hapmap];0.86[GIH][hapmap];1.00[TSI][hapmap]
rs297151	0.90[GIH][hapmap];0.82[JPT][hapmap]
rs297152	0.82[JPT][hapmap]
rs297153	0.87[CEU][hapmap];0.92[CHB][hapmap]
rs297158	1.00[CEU][hapmap];0.83[CHB][hapmap]
rs297159	0.87[CEU][hapmap];0.83[CHB][hapmap]
rs297160	0.85[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap]
rs371745	0.95[EUR][1000 genomes]
rs3765058	0.87[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs378698	0.87[CEU][hapmap];0.92[CHB][hapmap]
rs3796038	0.88[CEU][hapmap]
rs4142729	0.87[CEU][hapmap];0.92[CHB][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs422854	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs4643520	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4670270	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4670272	0.87[CEU][hapmap];0.83[CHB][hapmap]
rs4670901	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4670902	0.88[CEU][hapmap];0.84[CHB][hapmap];0.84[JPT][hapmap]
rs4670903	0.87[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs6419600	0.86[CEU][hapmap]
rs6544183	0.87[CEU][hapmap];0.92[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs6544184	0.98[EUR][1000 genomes]
rs6544185	0.87[CEU][hapmap];0.92[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs6544186	0.80[ASN][1000 genomes]
rs6544197	0.86[CEU][hapmap];0.89[CHB][hapmap]
rs6704656	0.87[CEU][hapmap];1.00[CHB][hapmap];0.98[EUR][1000 genomes]
rs6713281	0.87[CEU][hapmap];0.83[CHB][hapmap];0.86[GIH][hapmap];1.00[TSI][hapmap]
rs6716101	0.87[CEU][hapmap];1.00[CHB][hapmap];0.98[EUR][1000 genomes]
rs672208	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6725356	0.83[CHB][hapmap];1.00[TSI][hapmap]
rs6739568	0.83[CHB][hapmap]
rs6752850	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6756184	0.87[CEU][hapmap];0.83[CHB][hapmap]
rs6758330	0.84[GIH][hapmap]
rs7571052	0.87[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs7577088	0.87[CEU][hapmap];0.92[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs7582918	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7594644	0.93[EUR][1000 genomes]
rs958412	0.81[EUR][1000 genomes]
rs963730	0.88[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs963731	0.92[CHB][hapmap]
rs9679498	0.87[CEU][hapmap];0.83[CHB][hapmap];0.93[EUR][1000 genomes]
rs997344	0.83[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873884	chr2:39154463-39332093	Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv2755359	chr2:39169049-39417849	Strong transcription Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4670269	TMEM178	cis	cerebellum	SCAN
rs4670269	THUMPD2	cis	cerebellum	SCAN
rs4670269	ATL2	cis	parietal	SCAN
rs4670269	SOS1	Cis_1M	lymphoblastoid	RTeQTL
rs4670269	SOS1	cis	multi-tissue	Pritchard

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39188000-39199800	Weak transcription	Right Ventricle	heart
2	chr2:39188000-39202000	Weak transcription	Colon Smooth Muscle	Colon
3	chr2:39188000-39212400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr2:39188000-39212600	Weak transcription	Gastric	stomach
5	chr2:39188000-39213000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:39188000-39222400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr2:39188200-39201400	Weak transcription	Brain Angular Gyrus	brain
8	chr2:39188200-39201400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr2:39188200-39205000	Weak transcription	Fetal Brain Male	brain
10	chr2:39188200-39210800	Weak transcription	HMEC	breast
11	chr2:39188200-39211800	Weak transcription	Fetal Lung	lung
12	chr2:39188400-39201400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr2:39188400-39201600	Weak transcription	Brain Anterior Caudate	brain
14	chr2:39188400-39201600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr2:39188400-39212000	Weak transcription	Fetal Muscle Leg	muscle
16	chr2:39188400-39212400	Weak transcription	Fetal Brain Female	brain
17	chr2:39189200-39212000	Weak transcription	Fetal Muscle Trunk	muscle
18	chr2:39192000-39207400	Weak transcription	Fetal Intestine Small	intestine
19	chr2:39193000-39201600	Weak transcription	Brain Hippocampus Middle	brain
20	chr2:39194000-39202000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr2:39194000-39213000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr2:39194400-39218600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr2:39194600-39198400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr2:39194600-39199800	Weak transcription	Fetal Heart	heart
25	chr2:39194600-39212000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr2:39194600-39212800	Weak transcription	Spleen	Spleen
27	chr2:39195200-39198800	Strong transcription	Fetal Stomach	stomach
28	chr2:39195200-39210400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:39195400-39212600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr2:39196600-39199800	Weak transcription	Ovary	ovary
31	chr2:39196600-39203600	Weak transcription	Left Ventricle	heart
32	chr2:39196600-39212600	Weak transcription	Aorta	Aorta
33	chr2:39196800-39201600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr2:39197000-39225800	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr2:39197200-39211000	Weak transcription	Stomach Smooth Muscle	stomach
36	chr2:39197400-39210800	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr2:39197800-39198200	Strong transcription	Brain Germinal Matrix	brain
38	chr2:39198000-39198200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr2:39198000-39198200	Enhancers	H9 Cell Line	embryonic stem cell
40	chr2:39198000-39198600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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