Variant report

Variant	rs6427193
Chromosome Location	chr1:169448377-169448378
allele	C/T
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	POLR2A	chr1:169448250-169448547	IMR90	lung:	n/a	n/a
2	POLR2A	chr1:169447828-169448419	HepG2	liver:	n/a	n/a
3	KAP1	chr1:169448346-169448451	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:169445664..169448576-chr1:169507700..169509701,2	MCF-7	breast:
2	chr1:169447411..169449419-chr1:169497697..169499792,2	MCF-7	breast:
3	chr1:169336376..169338825-chr1:169448253..169450809,2	K562	blood:

Variant related genes	Relation type
ENSG00000234604	TF binding region
ENSG00000117475	Chromatin interaction
ENSG00000143156	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12118611	0.82[ASW][hapmap];0.81[MKK][hapmap]
rs12119479	0.82[ASW][hapmap];0.86[CEU][hapmap];0.95[GIH][hapmap];0.87[MKK][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs12121891	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs12124049	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs12128350	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12138875	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12143708	0.85[EUR][1000 genomes]
rs12730053	0.87[EUR][1000 genomes]
rs12750775	0.82[EUR][1000 genomes]
rs12758228	0.82[EUR][1000 genomes]
rs17577184	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs35010461	0.82[EUR][1000 genomes]
rs35107735	0.83[EUR][1000 genomes]
rs35220898	0.82[ASW][hapmap]
rs4589164	0.82[ASW][hapmap]
rs4656182	0.80[EUR][1000 genomes]
rs4656671	0.82[ASW][hapmap];0.86[CEU][hapmap];0.95[GIH][hapmap];0.87[MKK][hapmap];0.90[TSI][hapmap]
rs4656677	0.82[EUR][1000 genomes]
rs4656678	0.83[EUR][1000 genomes]
rs4656680	0.84[ASW][hapmap];0.86[CEU][hapmap];0.95[GIH][hapmap];0.87[MKK][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs61807017	0.80[EUR][1000 genomes]
rs6656463	1.00[ASW][hapmap];0.95[CEU][hapmap];0.90[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6692649	0.91[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6695137	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs722145	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7368145	0.81[EUR][1000 genomes]
rs7522896	0.84[CEU][hapmap]
rs7527703	0.82[ASW][hapmap];0.86[CEU][hapmap];0.95[GIH][hapmap];0.87[MKK][hapmap];0.90[TSI][hapmap]
rs7542751	0.89[CEU][hapmap]
rs7546347	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv831871	chr1:169320673-169486680	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1001454	chr1:169387381-169465274	Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv1005941	chr1:169410486-169456393	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6427193	NME7	Cis_1M	lymphoblastoid	RTeQTL
rs6427193	NME7	cis	cerebellum	SCAN
rs6427193	NME7	cis	Artery Tibial	GTEx
rs6427193	XCL2	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169430000-169450000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:169430000-169452000	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr1:169430000-169452000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr1:169430000-169452600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:169430000-169452800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:169430000-169452800	Weak transcription	Brain Germinal Matrix	brain
7	chr1:169430000-169452800	Weak transcription	HMEC	breast
8	chr1:169430000-169452800	Weak transcription	NHDF-Ad	bronchial
9	chr1:169430000-169452800	Weak transcription	NHEK	skin
10	chr1:169430000-169453400	Weak transcription	Colonic Mucosa	Colon
11	chr1:169430000-169453800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr1:169430000-169454000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:169430000-169454400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:169430000-169454400	Weak transcription	Spleen	Spleen
15	chr1:169430200-169450600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr1:169430200-169451800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:169430200-169452600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr1:169430200-169452600	Weak transcription	NH-A	brain
19	chr1:169430200-169453200	Weak transcription	Esophagus	oesophagus
20	chr1:169430600-169452800	Weak transcription	Small Intestine	intestine
21	chr1:169431200-169452000	Weak transcription	GM12878-XiMat	blood
22	chr1:169434600-169452600	Weak transcription	Primary B cells from cord blood	blood
23	chr1:169435200-169448400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:169435200-169452800	Weak transcription	Fetal Kidney	kidney
25	chr1:169435600-169449200	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr1:169437400-169450600	Weak transcription	Brain Angular Gyrus	brain
27	chr1:169437400-169452600	Weak transcription	HSMMtube	muscle
28	chr1:169437400-169452600	Weak transcription	Osteobl	bone
29	chr1:169437400-169452800	Weak transcription	Aorta	Aorta
30	chr1:169437400-169452800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr1:169437800-169452600	Weak transcription	Fetal Brain Female	brain
32	chr1:169438600-169452200	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr1:169438600-169453200	Weak transcription	Fetal Lung	lung
34	chr1:169438800-169452600	Weak transcription	HSMM	muscle
35	chr1:169439200-169452000	Weak transcription	Primary hematopoietic stem cells	blood
36	chr1:169439600-169452600	Weak transcription	Primary T cells from cord blood	blood
37	chr1:169443000-169452800	Weak transcription	A549	lung
38	chr1:169443800-169452800	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr1:169444200-169451800	Weak transcription	Brain Substantia Nigra	brain
40	chr1:169444200-169454000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr1:169444600-169452600	Weak transcription	Stomach Mucosa	stomach
42	chr1:169444600-169452800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr1:169444800-169449200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:169446600-169453000	Weak transcription	Colon Smooth Muscle	Colon
45	chr1:169446800-169448400	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr1:169446800-169448400	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr1:169446800-169448800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr1:169446800-169448800	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr1:169446800-169449800	Weak transcription	Adipose Nuclei	Adipose
50	chr1:169446800-169451000	Weak transcription	Left Ventricle	heart

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