Variant report

Variant	rs2172007
Chromosome Location	chr6:26639777-26639778
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF274	chr6:26638255-26640171	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:26639612..26641880-chr6:26658088..26660144,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000233631	TF binding region
ENSG00000181315	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1021372	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1021373	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1027203	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1027204	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10484442	0.82[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap]
rs1056667	0.84[GIH][hapmap]
rs1078679	0.82[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap]
rs10946835	0.85[GIH][hapmap]
rs12173982	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12526680	0.85[CHB][hapmap]
rs13207371	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1321479	0.82[GIH][hapmap]
rs1321482	0.87[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap]
rs1490488	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1535276	0.85[GIH][hapmap]
rs1570059	0.87[CHB][hapmap]
rs1570060	0.87[CHB][hapmap]
rs1570061	0.87[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap]
rs1884947	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2130657	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2224380	0.82[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap]
rs2393670	0.85[GIH][hapmap]
rs2451711	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2451712	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2451731	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2451740	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2451741	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2451744	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2451750	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2451751	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2494692	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2494700	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2494701	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2494709	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2494713	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2494716	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2498351	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2498380	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2504565	1.00[CEU][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes]
rs2504566	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2504567	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2504571	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2504592	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2504599	1.00[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap]
rs2504600	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2758383	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3001369	0.83[EUR][1000 genomes]
rs34453863	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3736781	0.83[GIH][hapmap]
rs3736782	0.85[GIH][hapmap]
rs3800303	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes]
rs4368798	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes]
rs4871	0.85[GIH][hapmap]
rs55930917	0.81[AFR][1000 genomes]
rs62394558	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6456733	0.82[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap]
rs6903973	0.84[GIH][hapmap]
rs6918360	0.87[CHB][hapmap]
rs6918506	0.87[CHB][hapmap]
rs6918854	0.87[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap]
rs6922824	0.82[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap]
rs6924865	0.82[GIH][hapmap]
rs6925087	0.83[EUR][1000 genomes]
rs6925703	0.85[GIH][hapmap]
rs6925895	0.82[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap]
rs6926629	0.85[GIH][hapmap]
rs6930120	0.82[CHB][hapmap]
rs6941022	0.82[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap]
rs767471	0.82[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap]
rs7753565	0.82[CHB][hapmap]
rs7767847	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[EUR][1000 genomes]
rs9295695	0.85[GIH][hapmap]
rs9295701	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9357010	0.85[GIH][hapmap]
rs9393729	0.85[GIH][hapmap]
rs9461270	0.85[GIH][hapmap]
rs9461271	0.82[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap]
rs9461272	0.87[CHB][hapmap]
rs9461273	0.96[CEU][hapmap];0.87[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.85[TSI][hapmap]
rs9461275	0.83[EUR][1000 genomes]
rs9461276	0.83[EUR][1000 genomes]
rs9461288	0.84[EUR][1000 genomes]
rs9467779	0.85[GIH][hapmap]
rs9467782	0.85[GIH][hapmap]
rs9467783	0.85[GIH][hapmap]
rs9467791	0.82[CHB][hapmap];0.84[GIH][hapmap]
rs9467798	0.82[CHB][hapmap]
rs9467800	0.87[CHB][hapmap]
rs9467810	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes]
rs9467813	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9986382	0.82[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap]

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	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs2172007	HCG11	Cis_1M	lymphoblastoid	RTeQTL
rs2172007	ZNF322	cis	Thyroid	GTEx
rs2172007	HIST1H2BD	cis	parietal	SCAN
rs2172007	ZNF322B	trans	lymphoblastoid	seeQTL
rs2172007	ZNF204P	cis	cerebellum	SCAN
rs2172007	ZNF204P	cis	parietal	SCAN
rs2172007	BTN3A1	cis	cerebellum	SCAN
rs2172007	ZNF322A	cis	multi-tissue	Pritchard
rs2172007	RP11-457M11.2	cis	Nerve Tibial	GTEx
rs2172007	RP11-457M11.2	cis	Thyroid	GTEx
rs2172007	BTN3A2	cis	lymphoblastoid	seeQTL
rs2172007	BTN3A3	cis	cerebellum	SCAN
rs2172007	ZNF322	cis	Artery Tibial	GTEx
rs2172007	HMGN4	Cis_1M	lymphoblastoid	RTeQTL
rs2172007	BTN3A3	cis	parietal	SCAN
rs2172007	BTN3A2	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26629800-26640000	Weak transcription	Left Ventricle	heart
2	chr6:26630400-26640000	Weak transcription	Aorta	Aorta
3	chr6:26631800-26640400	Weak transcription	Pancreas	Pancrea
4	chr6:26632000-26640600	Weak transcription	Fetal Stomach	stomach
5	chr6:26632600-26640000	Weak transcription	Fetal Kidney	kidney
6	chr6:26632800-26640000	Weak transcription	Esophagus	oesophagus
7	chr6:26633000-26640400	Weak transcription	Colon Smooth Muscle	Colon
8	chr6:26633000-26658000	Weak transcription	Fetal Brain Male	brain
9	chr6:26633200-26639800	Weak transcription	Gastric	stomach
10	chr6:26633200-26640000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr6:26633400-26640000	Weak transcription	Spleen	Spleen
12	chr6:26633400-26640600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr6:26633800-26640000	Weak transcription	Lung	lung
14	chr6:26634600-26639800	Weak transcription	Fetal Brain Female	brain
15	chr6:26634600-26639800	Weak transcription	Ovary	ovary
16	chr6:26634600-26640000	Weak transcription	Stomach Smooth Muscle	stomach
17	chr6:26636400-26645800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr6:26636800-26645800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
19	chr6:26637400-26640800	Weak transcription	Stomach Mucosa	stomach
20	chr6:26637600-26640000	Weak transcription	Brain Germinal Matrix	brain
21	chr6:26637600-26645800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr6:26638000-26640400	Weak transcription	Fetal Thymus	thymus
23	chr6:26638000-26645200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr6:26638200-26639800	Strong transcription	Skeletal Muscle Male	skeletal muscle
25	chr6:26638200-26640000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr6:26638200-26641800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr6:26638400-26640000	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr6:26638400-26643600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr6:26638400-26644800	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:26638400-26646800	ZNF genes & repeats	Liver	Liver
31	chr6:26638800-26640200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
32	chr6:26638800-26641400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
33	chr6:26638800-26641400	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
34	chr6:26638800-26641600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
35	chr6:26638800-26641600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr6:26638800-26641800	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr6:26638800-26642600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
38	chr6:26638800-26644400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
39	chr6:26638800-26644800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr6:26638800-26645400	ZNF genes & repeats	Primary B cells from cord blood	blood
41	chr6:26638800-26645600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr6:26638800-26646600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr6:26638800-26646800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr6:26638800-26646800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr6:26639000-26639800	Strong transcription	Brain Substantia Nigra	brain
46	chr6:26639000-26640000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr6:26639000-26640200	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr6:26639000-26640200	ZNF genes & repeats	Adipose Nuclei	Adipose
49	chr6:26639000-26640600	Strong transcription	Hela-S3	cervix
50	chr6:26639000-26640800	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 2	blood

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