Variant report

Variant	rs9614006
Chromosome Location	chr22:30004929-30004930
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:29999342..30001478-chr22:30003978..30005588,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CABP7-2	chr22:30004889-30005490	NONHSAT084715

Variant related genes	Relation type
ENSG00000186575	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1058642	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11090569	0.81[EUR][1000 genomes]
rs12172347	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12484392	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13054618	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13055568	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13055746	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13056992	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13057041	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1800538	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1807506	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2024116	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2024119	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2024121	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2072301	0.96[CEU][hapmap]
rs2240638	0.95[CEU][hapmap];0.88[JPT][hapmap];0.84[YRI][hapmap];0.81[EUR][1000 genomes]
rs2245185	0.87[LWK][hapmap]
rs2267147	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2348672	0.80[EUR][1000 genomes]
rs2348677	0.80[EUR][1000 genomes]
rs2348683	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2348684	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2530670	0.88[LWK][hapmap]
rs34013089	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35404981	0.80[EUR][1000 genomes]
rs3940296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4470427	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67292640	0.81[EUR][1000 genomes]
rs67884471	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs715490	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7287318	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs737975	0.96[CEU][hapmap]
rs737980	1.00[ASW][hapmap];0.96[CEU][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.80[EUR][1000 genomes]
rs737981	0.80[EUR][1000 genomes]
rs8142111	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs867088	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9608781	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9608785	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9608787	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9608789	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9608790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9608794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9608798	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9608799	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9613940	0.83[ASW][hapmap];0.96[CEU][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes]
rs9613942	0.83[ASW][hapmap];0.96[CEU][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes]
rs9613943	0.80[EUR][1000 genomes]
rs9613956	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9613957	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9613958	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9613961	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9613963	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9613965	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9613970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613977	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613978	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9613979	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9613980	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9613983	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9613984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613986	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613990	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613991	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613992	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9613993	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613994	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613995	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9613996	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613997	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9613998	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9613999	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9614004	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9614005	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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]
rs9614011	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9614014	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9614018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs999458	0.82[JPT][hapmap];0.85[YRI][hapmap];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1058156	chr22:29772043-30024013	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv544675	chr22:29772043-30024013	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv1062373	chr22:29826745-30092448	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv544676	chr22:29826745-30092448	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
8	nsv834172	chr22:29899036-30057948	Strong transcription Weak transcription Flanking Active TSS Enhancers 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	16 gene(s)	inside rSNPs	diseases
9	nsv817417	chr22:29998464-30035142	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs9614006	NEFH	cis	multi-tissue	Pritchard
rs9614006	THOC5	cis	Thyroid	GTEx
rs9614006	THOC5	cis	Adipose Subcutaneous	GTEx
rs9614006	NIPSNAP1	cis	parietal	SCAN
rs9614006	NIPSNAP1	cis	lymphoblastoid	seeQTL
rs9614006	NF2	cis	parietal	SCAN
rs9614006	THOC5	cis	Artery Tibial	GTEx

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30000400-30026600	Weak transcription	Gastric	stomach
2	chr22:30001000-30013400	Weak transcription	Fetal Kidney	kidney
3	chr22:30001000-30019400	Weak transcription	Thymus	Thymus
4	chr22:30001200-30005400	Weak transcription	Aorta	Aorta
5	chr22:30001200-30006600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr22:30001200-30013800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr22:30001400-30005200	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr22:30001400-30005800	Weak transcription	Fetal Intestine Large	intestine
9	chr22:30001400-30006600	Weak transcription	Primary B cells from peripheral blood	blood
10	chr22:30001400-30013400	Weak transcription	Brain Angular Gyrus	brain
11	chr22:30001400-30013400	Weak transcription	Ovary	ovary
12	chr22:30001400-30013400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr22:30001400-30014000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr22:30001600-30005000	Weak transcription	K562	blood
15	chr22:30001600-30005400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr22:30001600-30006400	Weak transcription	Liver	Liver
17	chr22:30001600-30013400	Weak transcription	Fetal Lung	lung
18	chr22:30001600-30013600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr22:30002000-30005400	Weak transcription	Brain Germinal Matrix	brain
20	chr22:30002000-30005600	Enhancers	HUVEC	blood vessel
21	chr22:30002000-30006000	Weak transcription	Fetal Thymus	thymus
22	chr22:30002000-30006400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr22:30002000-30008400	Weak transcription	Hela-S3	cervix
24	chr22:30002000-30013400	Weak transcription	Small Intestine	intestine
25	chr22:30002000-30014200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr22:30002000-30017600	Weak transcription	Primary T cells from cord blood	blood
27	chr22:30002200-30013600	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr22:30002400-30011200	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr22:30002400-30011600	Weak transcription	NHLF	lung
30	chr22:30002400-30013000	Weak transcription	HMEC	breast
31	chr22:30002400-30013600	Weak transcription	HSMMtube	muscle
32	chr22:30002400-30013800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr22:30002600-30005000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr22:30002600-30005200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr22:30002600-30005400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr22:30002600-30007200	Weak transcription	Fetal Intestine Small	intestine
37	chr22:30002600-30011200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr22:30002600-30013400	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr22:30002600-30013400	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr22:30002600-30013400	Weak transcription	Colon Smooth Muscle	Colon
41	chr22:30002600-30013400	Weak transcription	Stomach Smooth Muscle	stomach
42	chr22:30002600-30013400	Weak transcription	HSMM	muscle
43	chr22:30002600-30014000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr22:30002800-30005000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr22:30002800-30005000	Weak transcription	HepG2	liver
46	chr22:30002800-30005400	Weak transcription	GM12878-XiMat	blood
47	chr22:30002800-30013600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr22:30002800-30017600	Weak transcription	Lung	lung
49	chr22:30003000-30006000	Weak transcription	Fetal Muscle Leg	muscle
50	chr22:30003000-30006000	Weak transcription	Fetal Stomach	stomach

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