Variant report

Variant	rs348196
Chromosome Location	chr1:155666961-155666962
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:155098358..155100782-chr1:155664787..155667283,2	K562	blood:
2	chr1:155656565..155660782-chr1:155662182..155667108,10	MCF-7	breast:
3	chr1:155656893..155661917-chr1:155662515..155668604,13	MCF-7	breast:

Variant related genes	Relation type
ENSG00000132676	Chromatin interaction
ENSG00000169242	Chromatin interaction
ENSG00000163374	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10752611	0.80[CEU][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap]
rs10908469	0.91[JPT][hapmap]
rs10908470	0.80[CEU][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap]
rs10908471	0.80[CEU][hapmap];0.91[JPT][hapmap]
rs10908479	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10908481	0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10908482	0.80[ASN][1000 genomes]
rs11264380	0.80[CEU][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap]
rs11264381	0.80[CEU][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap]
rs11264387	0.80[CEU][hapmap];0.88[GIH][hapmap]
rs11264397	0.83[ASN][1000 genomes]
rs11264398	0.80[EUR][1000 genomes]
rs11264409	0.80[ASN][1000 genomes]
rs12035524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12039893	0.83[ASN][1000 genomes]
rs12040100	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12047756	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12091730	0.87[EUR][1000 genomes]
rs12143948	0.91[JPT][hapmap]
rs12740629	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12744132	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12746592	0.80[CEU][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap]
rs12758945	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1360554	0.91[JPT][hapmap]
rs1556488	0.80[CEU][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap]
rs2048431	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2175391	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]
rs2666826	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28662267	0.83[ASN][1000 genomes]
rs34620961	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs348186	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs348192	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35615695	0.91[JPT][hapmap]
rs3738590	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3820594	0.80[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap]
rs3892792	0.80[CEU][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap]
rs4278368	0.81[ASN][1000 genomes]
rs4550031	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs475550	1.00[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[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];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs490608	0.85[ASN][1000 genomes]
rs4971095	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6427286	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs644853	0.91[JPT][hapmap]
rs6665227	0.80[ASN][1000 genomes]
rs6672128	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6688636	0.91[JPT][hapmap]
rs6696888	0.91[JPT][hapmap]
rs670876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs678157	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs708611	0.85[CHB][hapmap];0.97[CHD][hapmap]
rs7521594	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7541060	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs821551	0.91[JPT][hapmap]
rs822490	0.80[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap]
rs860295	0.85[CHB][hapmap];0.97[CHD][hapmap];0.82[JPT][hapmap]
rs9426933	0.84[ASN][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	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	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	nsv3054	chr1:155653835-155673509	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	n/a
12	esv3423892	chr1:155664084-155901487	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs348196	YY1AP1	cis	parietal	SCAN
rs348196	GPATCH4	cis	parietal	SCAN
rs348196	GBAP1	cis	cerebellum	SCAN
rs348196	FDPS	cis	parietal	SCAN
rs348196	LCE1F	cis	cerebellum	SCAN
rs348196	LCE1C	cis	parietal	SCAN
rs348196	ADAM15	cis	multi-tissue	Pritchard
rs348196	YY1AP1	cis	cerebellum	SCAN
rs348196	SPRR2D	cis	parietal	SCAN
rs348196	GBAP1	cis	parietal	SCAN
rs348196	RIT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155659400-155668200	Weak transcription	Aorta	Aorta
2	chr1:155660000-155667600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:155660200-155667000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
4	chr1:155660200-155667000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:155660200-155668000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:155660200-155698800	Weak transcription	NHLF	lung
7	chr1:155660400-155668400	Weak transcription	Fetal Intestine Large	intestine
8	chr1:155660400-155671000	Weak transcription	Esophagus	oesophagus
9	chr1:155660400-155675000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:155660400-155682800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr1:155660400-155688800	Weak transcription	Lung	lung
12	chr1:155660400-155706200	Weak transcription	Colonic Mucosa	Colon
13	chr1:155660600-155668000	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr1:155660600-155679000	Weak transcription	Fetal Brain Female	brain
15	chr1:155660600-155680200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr1:155660800-155682600	Weak transcription	Spleen	Spleen
17	chr1:155661600-155688600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr1:155661600-155707800	Weak transcription	HUVEC	blood vessel
19	chr1:155661800-155668400	Weak transcription	NH-A	brain
20	chr1:155662200-155669400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr1:155662200-155682000	Weak transcription	HSMMtube	muscle
22	chr1:155662400-155667000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:155662400-155668400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr1:155662400-155682800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr1:155662400-155685600	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr1:155662600-155667000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:155662600-155667000	Weak transcription	Fetal Muscle Trunk	muscle
28	chr1:155662600-155669200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:155662600-155673800	Weak transcription	HMEC	breast
30	chr1:155662800-155668200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr1:155663000-155679400	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr1:155663000-155681200	Weak transcription	Duodenum Mucosa	Duodenum
33	chr1:155663200-155667200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:155663200-155668200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr1:155663200-155668200	Weak transcription	Osteobl	bone
36	chr1:155663200-155668600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:155663200-155675800	Weak transcription	HSMM	muscle
38	chr1:155663200-155679200	Weak transcription	Primary B cells from peripheral blood	blood
39	chr1:155663200-155701000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr1:155663400-155682600	Weak transcription	Primary B cells from cord blood	blood
41	chr1:155664400-155674600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr1:155664400-155678800	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr1:155664400-155679000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr1:155664600-155667200	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr1:155664800-155667800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr1:155665000-155673600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:155665000-155678600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr1:155665200-155667000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:155665200-155667200	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr1:155665200-155667200	Enhancers	Brain Germinal Matrix	brain

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