Variant report

Variant	rs2968559
Chromosome Location	chr7:140371545-140371546
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:140370608..140383131-chr7:140387718..140398587,28	MCF-7	breast:
2	chr7:140371506..140376729-chr7:140377280..140380130,6	K562	blood:
3	chr7:140371233..140372859-chr7:140417535..140420248,2	MCF-7	breast:
4	chr7:140371193..140374993-chr7:140376654..140380151,6	MCF-7	breast:
5	chr7:140358444..140360553-chr7:140370671..140372780,2	MCF-7	breast:
6	chr7:140366280..140367939-chr7:140371289..140372844,2	MCF-7	breast:
7	chr7:140370275..140375389-chr7:140393210..140401279,16	MCF-7	breast:

Variant related genes	Relation type
ENSG00000133597	Chromatin interaction
ENSG00000240889	Chromatin interaction
ENSG00000090266	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10228254	0.85[ASN][1000 genomes]
rs10241711	0.83[CHB][hapmap]
rs10258462	0.85[ASN][1000 genomes]
rs10258465	0.85[ASN][1000 genomes]
rs10260676	0.83[ASN][1000 genomes]
rs1140034	0.94[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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12375245	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs1267600	0.91[CHB][hapmap]
rs1267601	0.91[CHB][hapmap]
rs1267606	0.91[CHB][hapmap]
rs1267611	0.81[CHB][hapmap]
rs1267613	0.81[CHB][hapmap]
rs1267619	0.91[CHB][hapmap]
rs1267636	0.81[CHB][hapmap]
rs1267638	0.91[CHB][hapmap]
rs1267642	0.81[CHB][hapmap]
rs1267643	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs1267644	0.81[CHB][hapmap]
rs1267649	0.91[CHB][hapmap]
rs1639675	0.91[CHB][hapmap]
rs1639678	0.91[CHB][hapmap]
rs1639679	0.81[CHB][hapmap]
rs17161666	0.83[CHB][hapmap]
rs17161668	0.81[ASN][1000 genomes]
rs17161750	0.91[CHB][hapmap]
rs1733827	0.91[CHB][hapmap]
rs1733832	0.91[CHB][hapmap]
rs2364393	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2364394	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2364395	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2364396	0.83[CHB][hapmap]
rs2364397	0.94[ASW][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];0.81[ASN][1000 genomes]
rs2364399	0.80[MKK][hapmap]
rs2535951	0.91[CHB][hapmap]
rs28517771	0.90[ASN][1000 genomes]
rs2907950	0.89[ASN][1000 genomes]
rs2930315	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2930318	0.94[ASN][1000 genomes]
rs2930319	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2930328	0.89[MKK][hapmap]
rs2930329	0.89[MKK][hapmap]
rs2930331	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2968549	0.87[ASN][1000 genomes]
rs2968550	0.94[ASW][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];0.87[ASN][1000 genomes]
rs2968551	0.92[ASN][1000 genomes]
rs2968553	0.94[ASW][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2968555	0.96[ASN][1000 genomes]
rs2968558	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4624945	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4725799	0.81[ASN][1000 genomes]
rs4727011	0.89[ASW][hapmap];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];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4727021	0.81[ASN][1000 genomes]
rs4727036	0.81[ASN][1000 genomes]
rs4727040	0.83[CHB][hapmap]
rs4727041	0.83[CHB][hapmap]
rs6464036	0.91[CHB][hapmap]
rs6464937	0.94[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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6977834	0.87[ASN][1000 genomes]
rs73505645	0.90[ASN][1000 genomes]
rs73505647	0.88[ASN][1000 genomes]
rs7792746	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7794857	0.85[ASN][1000 genomes]
rs7802537	0.83[ASW][hapmap]
rs7803697	0.94[ASW][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];0.87[ASN][1000 genomes]
rs7809339	0.81[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831157	chr7:140241339-140426876	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2968559	NDUFB2	cis	lymphoblastoid	seeQTL
rs2968559	DGKI	cis	cerebellum	SCAN
rs2968559	ADCK2	Cis_1M	lymphoblastoid	RTeQTL
rs2968559	TMEM139	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140365800-140372000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr7:140367400-140371800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr7:140368000-140371800	Weak transcription	Fetal Kidney	kidney
4	chr7:140369200-140371600	Weak transcription	Ovary	ovary
5	chr7:140369600-140372000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr7:140370000-140371800	Weak transcription	Placenta	Placenta
7	chr7:140370400-140371800	Weak transcription	Hela-S3	cervix
8	chr7:140370400-140372000	Weak transcription	A549	lung
9	chr7:140370600-140371600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr7:140370600-140371800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr7:140370600-140371800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr7:140370600-140372200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr7:140370800-140372000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr7:140370800-140372000	Weak transcription	K562	blood
15	chr7:140371000-140372400	Weak transcription	NHLF	lung
16	chr7:140371200-140371600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr7:140371400-140371600	Enhancers	iPS-15b Cell Line	embryonic stem cell

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