Variant report

Variant	rs149946
Chromosome Location	chr6:27970031-27970032
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:27940946..27942565-chr6:27968456..27970248,2	K562	blood:
2	chr6:27969309..27971948-chr6:27974273..27976504,2	K562	blood:
3	chr6:27969301..27971471-chr6:27975045..27977766,2	K562	blood:

Extended variants
information (count: 122 )
Associated
traits (count: 27 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs1150666	0.82[YRI][hapmap]
rs1150689	0.95[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap]
rs12174753	1.00[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap]
rs1225598	0.95[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap]
rs1225599	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap]
rs1233699	0.95[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap]
rs1233701	0.95[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap]
rs1233704	0.95[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap]
rs1233705	0.95[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap]
rs1340004	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs149897	0.94[ASW][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap]
rs149899	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs149900	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs149942	0.94[ASW][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap]
rs149944	0.81[CHB][hapmap];1.00[YRI][hapmap]
rs149945	0.81[CHB][hapmap];1.00[YRI][hapmap]
rs149947	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs149948	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs149955	0.81[CHB][hapmap];1.00[YRI][hapmap]
rs149959	0.81[CHB][hapmap];1.00[YRI][hapmap]
rs149961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs149964	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs149968	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs149969	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs149970	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs149972	0.81[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs149989	0.81[CHB][hapmap];1.00[YRI][hapmap]
rs156736	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs156739	0.81[CHB][hapmap];1.00[YRI][hapmap]
rs156744	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1631552	0.90[YRI][hapmap]
rs16893666	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs172166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs175954	0.85[EUR][1000 genomes]
rs1770131	0.90[YRI][hapmap]
rs17711344	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs17711801	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs17774663	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs183244	0.81[CHB][hapmap];1.00[YRI][hapmap]
rs1853097	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs188105	0.89[YRI][hapmap]
rs1904840	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs1904841	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs1947862	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs1947863	0.81[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap]
rs200969	0.95[CEU][hapmap]
rs200994	0.90[CEU][hapmap]
rs203876	0.90[YRI][hapmap]
rs203877	0.90[YRI][hapmap]
rs203882	0.90[YRI][hapmap]
rs203884	0.90[YRI][hapmap]
rs203890	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs203893	0.90[YRI][hapmap]
rs2116984	0.80[YRI][hapmap]
rs2275508	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs2281588	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2295594	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2622319	0.82[YRI][hapmap]
rs3173443	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs34171748	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3734573	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs3823180	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs464312	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs469227	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4711165	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs4713135	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs4713137	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs4713142	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs4713143	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs4713144	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs4713145	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs4713148	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs4713152	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs536704	0.81[CEU][hapmap];0.89[YRI][hapmap]
rs573179	0.95[CEU][hapmap]
rs66529373	0.81[EUR][1000 genomes]
rs6901017	0.81[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap]
rs6922063	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs6931858	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap]
rs6932109	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs6941992	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs7755442	1.00[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap]
rs868987	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs9283884	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs9295758	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs9295759	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap]
rs9295760	0.84[CEU][hapmap]
rs9295761	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs9295762	0.95[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap]
rs9348789	0.82[EUR][1000 genomes]
rs9348793	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs9348794	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs9348796	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs9357060	0.82[EUR][1000 genomes]
rs9368553	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs9368554	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs9368555	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap]
rs9368560	0.90[CEU][hapmap]
rs9380045	0.82[EUR][1000 genomes]
rs9380047	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap]
rs9380052	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap]
rs9380055	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs9380057	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs9380059	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs9380062	1.00[CEU][hapmap]
rs9393881	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap];0.82[EUR][1000 genomes]
rs9393890	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs9393892	0.81[CHB][hapmap]
rs9393893	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs9393897	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs9393901	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs9461433	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs9468271	0.82[EUR][1000 genomes]
rs9468274	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs9468275	0.82[EUR][1000 genomes]
rs9468277	0.82[EUR][1000 genomes]
rs9468278	0.82[EUR][1000 genomes]
rs9468286	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs9468298	0.90[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432858	chr6:27719375-28011652	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	387 gene(s)	inside rSNPs	diseases
2	nsv1022651	chr6:27864217-28017997	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv830619	chr6:27872302-28062544	Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:27)

SNP	Gene	Cis/trans	Tissue	Source
rs149946	ZNF323	cis	Temporal Cortex	GTEx
rs149946	RP1-265C24.5	cis	Heart Left Ventricle	GTEx
rs149946	ZNF204P	cis	parietal	SCAN
rs149946	ZNF323	cis	parietal	SCAN
rs149946	NKAPL	cis	parietal	SCAN
rs149946	RP1-265C24.5	cis	Muscle Skeletal	GTEx
rs149946	AL022393.7	cis	Artery Aorta	GTEx
rs149946	ZNF192	cis	cerebellum	SCAN
rs149946	ZNF323	cis	Brain Pons	GTEx
rs149946	ZNF323	cis	cerebellum	SCAN
rs149946	ZSCAN23	cis	cerebellum	SCAN
rs149946	LRRC16A	cis	parietal	SCAN
rs149946	HIST1H2BC	cis	parietal	SCAN
rs149946	BTN3A2	cis	multi-tissue	Pritchard
rs149946	AL022393.7	cis	Muscle Skeletal	GTEx
rs149946	BTN2A1	cis	cerebellum	SCAN
rs149946	OR2B8P	cis	Thyroid	GTEx
rs149946	OR2B7P	cis	Thyroid	GTEx
rs149946	AL022393.7	cis	Nerve Tibial	GTEx
rs149946	ZNF187	cis	cerebellum	SCAN
rs149946	ZNF187	cis	parietal	SCAN
rs149946	ZSCAN23	cis	parietal	SCAN
rs149946	ZNF323	cis	Frontal Cortex	GTEx
rs149946	ZNF192	cis	parietal	SCAN
rs149946		cis	Lymphoblastoid	GTEx
rs149946	ZKSCAN3	cis	parietal	SCAN
rs149946	BTN2A1	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27966600-27970600	Weak transcription	Right Atrium	heart
2	chr6:27968800-27970200	Enhancers	Placenta	Placenta
3	chr6:27969200-27970200	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr6:27969200-27971800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr6:27969200-27971800	Weak transcription	K562	blood
6	chr6:27969600-27970200	Enhancers	H1 Cell Line	embryonic stem cell
7	chr6:27969600-27970200	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr6:27969800-27972200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr6:27970000-27970200	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr6:27970000-27970400	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr6:27970000-27971000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr6:27970000-27971000	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr6:27970000-27971200	Enhancers	Rectal Mucosa Donor 29	rectum

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