Variant report

Variant	rs2175391
Chromosome Location	chr1:155625602-155625603
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:155625229..155627200-chr1:155627769..155629453,2	K562	blood:
2	chr1:155624881..155626897-chr1:155647501..155650003,2	K562	blood:
3	chr1:155619254..155623405-chr1:155624294..155627558,5	K562	blood:
4	chr1:155623481..155626376-chr1:155629925..155633670,3	K562	blood:
5	chr1:155619254..155623405-chr1:155624023..155627558,4	K562	blood:

Variant related genes	Relation type
ENSG00000246203	Chromatin interaction
ENSG00000163374	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10752611	0.96[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs10796945	0.88[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.94[TSI][hapmap]
rs10908469	0.92[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap]
rs10908470	0.96[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs10908471	0.96[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes]
rs10908472	0.89[EUR][1000 genomes]
rs10908479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10908481	0.88[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap]
rs11264380	0.96[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs11264381	0.96[CEU][hapmap];0.85[CHB][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs11264383	0.89[EUR][1000 genomes]
rs11264386	0.92[EUR][1000 genomes]
rs11264387	0.96[CEU][hapmap];0.81[CHB][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes]
rs11264393	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11264397	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11264398	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12022088	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12030596	0.88[EUR][1000 genomes]
rs12035524	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12039893	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12040100	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12047626	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12047756	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12079134	0.92[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap]
rs12093350	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12143948	0.81[CHB][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap]
rs12724079	0.81[CHB][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap]
rs12740629	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12744132	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12746592	0.96[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs12758945	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1360554	0.81[CHB][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap]
rs1556488	0.96[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap]
rs2048431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2666826	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs28662267	0.81[EUR][1000 genomes]
rs34124416	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34620961	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34632540	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs348186	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs348192	0.82[AMR][1000 genomes]
rs348196	1.00[ASW][hapmap];0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35615695	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs3738590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3851912	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3892792	0.96[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs4550031	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs475550	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4971095	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6427278	0.91[EUR][1000 genomes]
rs6427286	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs644853	0.91[JPT][hapmap]
rs6672128	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6688636	0.81[CHB][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap]
rs6696888	0.81[CHB][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap]
rs670876	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs678157	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs708611	0.85[CHB][hapmap];0.97[CHD][hapmap]
rs7411786	0.84[EUR][1000 genomes]
rs7521594	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7541060	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs821551	0.91[JPT][hapmap]
rs822490	0.95[CHD][hapmap];0.82[JPT][hapmap]
rs860295	0.85[CHB][hapmap];0.97[CHD][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529709	chr1:155154933-155757219	Strong transcription Weak transcription Flanking Active TSS Enhancers 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	450 gene(s)	inside rSNPs	diseases
2	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	esv3431739	chr1:155514331-155664183	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer 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	61 gene(s)	inside rSNPs	diseases
4	esv3388968	chr1:155532335-155658278	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised 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	55 gene(s)	inside rSNPs	diseases
5	nsv1002390	chr1:155553423-155706930	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv428246	chr1:155558197-155785831	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv436522	chr1:155559513-155674249	Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv946419	chr1:155561148-155630744	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription 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	23 gene(s)	inside rSNPs	diseases
9	esv3360339	chr1:155562157-155683127	Active TSS Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
10	nsv547965	chr1:155563152-155688600	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
11	esv3381327	chr1:155582853-155718436	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
12	esv3436971	chr1:155618172-155733386	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
13	esv3338099	chr1:155618190-155733359	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2175391	YY1AP1	cis	cerebellum	SCAN
rs2175391	RIT1	cis	cerebellum	SCAN
rs2175391	ADAM15	cis	multi-tissue	Pritchard
rs2175391	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs2175391	THEM5	cis	parietal	SCAN
rs2175391	GPATCH4	cis	parietal	SCAN
rs2175391	SPRR2A	cis	cerebellum	SCAN
rs2175391	FDPS	cis	parietal	SCAN
rs2175391	YY1AP1	cis	parietal	SCAN
rs2175391	FDPS	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155615400-155628600	Weak transcription	Right Ventricle	heart
2	chr1:155615600-155628400	Weak transcription	Left Ventricle	heart
3	chr1:155615600-155628400	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr1:155616000-155628200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr1:155616400-155628800	Weak transcription	Small Intestine	intestine
6	chr1:155617000-155628400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:155617800-155637000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr1:155618600-155628000	Weak transcription	Fetal Thymus	thymus
9	chr1:155618800-155627000	Weak transcription	Fetal Stomach	stomach
10	chr1:155618800-155628000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:155618800-155628000	Weak transcription	Brain Germinal Matrix	brain
12	chr1:155618800-155628400	Weak transcription	Colon Smooth Muscle	Colon
13	chr1:155618800-155628400	Weak transcription	Fetal Lung	lung
14	chr1:155618800-155628800	Weak transcription	Colonic Mucosa	Colon
15	chr1:155618800-155631800	Weak transcription	K562	blood
16	chr1:155619000-155627600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:155619000-155628000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:155619000-155628000	Weak transcription	Liver	Liver
19	chr1:155620400-155627800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:155620600-155628200	Weak transcription	Ovary	ovary
21	chr1:155620800-155628200	Weak transcription	Brain Hippocampus Middle	brain
22	chr1:155620800-155628400	Weak transcription	Psoas Muscle	Psoas
23	chr1:155621000-155628200	Weak transcription	Fetal Brain Male	brain
24	chr1:155621000-155628200	Weak transcription	Lung	lung
25	chr1:155621200-155628000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:155621400-155628200	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr1:155621400-155628200	Weak transcription	Duodenum Mucosa	Duodenum
28	chr1:155621600-155628000	Weak transcription	Adipose Nuclei	Adipose
29	chr1:155621600-155628000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr1:155621600-155628000	Weak transcription	Stomach Smooth Muscle	stomach
31	chr1:155621600-155628200	Weak transcription	Fetal Brain Female	brain
32	chr1:155621600-155628400	Weak transcription	Rectal Smooth Muscle	rectum
33	chr1:155621600-155628800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr1:155621800-155628200	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr1:155621800-155628400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:155621800-155628400	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr1:155621800-155628800	Weak transcription	Aorta	Aorta
38	chr1:155622000-155627200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr1:155622000-155628000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr1:155622000-155628000	Weak transcription	Esophagus	oesophagus
41	chr1:155622000-155628000	Weak transcription	Placenta	Placenta
42	chr1:155622000-155628400	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr1:155622000-155628400	Weak transcription	NH-A	brain
44	chr1:155622200-155627600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr1:155622200-155628000	Weak transcription	Primary hematopoietic stem cells	blood
46	chr1:155622200-155628000	Weak transcription	HSMM	muscle
47	chr1:155622200-155628200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr1:155622200-155628200	Weak transcription	HSMMtube	muscle
49	chr1:155622200-155628400	Weak transcription	NHLF	lung
50	chr1:155622400-155628200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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