Variant report

Variant	rs1997679
Chromosome Location	chr6:15658905-15658906
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:15652481..15654857-chr6:15657741..15659899,3	K562	blood:
2	chr6:15655170..15659272-chr6:15659508..15662983,5	MCF-7	breast:
3	chr6:15628579..15630551-chr6:15656798..15659188,2	K562	blood:
4	chr6:15657500..15659223-chr6:15666722..15668599,2	K562	blood:

Extended variants
information (count: 96 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1018381	1.00[ASN][1000 genomes]
rs1018382	1.00[ASN][1000 genomes]
rs1040410	0.83[ASN][1000 genomes]
rs10949305	0.83[ASN][1000 genomes]
rs11752196	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11752598	0.95[ASN][1000 genomes]
rs11755055	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11757499	1.00[ASN][1000 genomes]
rs11759609	1.00[ASN][1000 genomes]
rs16876671	1.00[ASN][1000 genomes]
rs2205852	0.95[ASN][1000 genomes]
rs2619516	1.00[ASN][1000 genomes]
rs2619519	1.00[ASN][1000 genomes]
rs2619521	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2619522	0.82[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2619524	0.81[ASN][1000 genomes]
rs2619525	0.81[ASN][1000 genomes]
rs2619526	1.00[ASN][1000 genomes]
rs2619528	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2619529	1.00[ASN][1000 genomes]
rs2619530	0.95[ASN][1000 genomes]
rs2619533	0.95[ASN][1000 genomes]
rs2619534	0.95[ASN][1000 genomes]
rs2619535	1.00[ASN][1000 genomes]
rs2619540	1.00[ASN][1000 genomes]
rs2619541	1.00[ASN][1000 genomes]
rs2619544	1.00[ASN][1000 genomes]
rs2619545	0.82[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2619546	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2619547	0.81[ASN][1000 genomes]
rs2619548	1.00[ASN][1000 genomes]
rs2619552	1.00[ASN][1000 genomes]
rs2743548	1.00[ASN][1000 genomes]
rs2743549	1.00[ASN][1000 genomes]
rs2743550	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[ASN][1000 genomes]
rs2743551	0.95[ASN][1000 genomes]
rs2743552	0.95[ASN][1000 genomes]
rs2743553	0.95[ASN][1000 genomes]
rs2743853	1.00[ASN][1000 genomes]
rs2743854	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2743856	0.81[ASN][1000 genomes]
rs2743857	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2743858	1.00[ASN][1000 genomes]
rs2743859	1.00[ASN][1000 genomes]
rs2743860	1.00[ASN][1000 genomes]
rs2743861	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2743864	1.00[ASN][1000 genomes]
rs2743865	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2743866	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2743867	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2743869	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2743870	1.00[ASN][1000 genomes]
rs2743871	1.00[ASN][1000 genomes]
rs2743872	1.00[ASN][1000 genomes]
rs6459408	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6903159	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs734129	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs760761	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7752070	1.00[ASN][1000 genomes]
rs7770921	1.00[ASN][1000 genomes]
rs875463	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9296979	0.83[ASN][1000 genomes]
rs9296984	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9296985	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9296987	1.00[ASN][1000 genomes]
rs9296988	1.00[ASN][1000 genomes]
rs9464797	0.87[ASN][1000 genomes]
rs9464801	1.00[ASN][1000 genomes]
rs9464802	1.00[ASN][1000 genomes]
rs9464803	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9464805	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9464807	1.00[ASN][1000 genomes]
rs9476835	0.83[ASN][1000 genomes]
rs9476837	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs9476838	1.00[JPT][hapmap]
rs9476839	0.85[ASN][1000 genomes]
rs9476841	0.85[ASN][1000 genomes]
rs9476842	0.83[ASN][1000 genomes]
rs9476844	0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9476845	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9476846	0.95[ASN][1000 genomes]
rs9476849	0.95[ASN][1000 genomes]
rs9476854	1.00[ASN][1000 genomes]
rs9476858	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9476859	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9476860	1.00[ASN][1000 genomes]
rs9476863	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9476865	1.00[ASN][1000 genomes]
rs9476866	1.00[ASN][1000 genomes]
rs9476867	1.00[ASN][1000 genomes]
rs9476868	1.00[ASN][1000 genomes]
rs9476869	1.00[ASN][1000 genomes]
rs9476883	1.00[ASN][1000 genomes]

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	nsv428136	chr6:15595640-15781241	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv2755670	chr6:15624762-15736008	Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv3414662	chr6:15655007-15660306	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1997679	RNF144B	cis	parietal	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15600000-15660400	Weak transcription	Hela-S3	cervix
2	chr6:15615200-15662200	Weak transcription	Gastric	stomach
3	chr6:15616800-15662000	Weak transcription	Placenta	Placenta
4	chr6:15616800-15662200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:15621800-15662200	Weak transcription	Pancreas	Pancrea
6	chr6:15623800-15662000	Weak transcription	Stomach Smooth Muscle	stomach
7	chr6:15628600-15662000	Weak transcription	NHLF	lung
8	chr6:15629600-15661800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr6:15632200-15662000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr6:15637200-15662000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr6:15638200-15662000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr6:15639400-15662200	Weak transcription	Left Ventricle	heart
13	chr6:15642000-15662000	Weak transcription	Brain Angular Gyrus	brain
14	chr6:15642200-15662200	Weak transcription	Aorta	Aorta
15	chr6:15642400-15661400	Weak transcription	Spleen	Spleen
16	chr6:15642600-15662200	Weak transcription	Esophagus	oesophagus
17	chr6:15642800-15662000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr6:15642800-15662000	Weak transcription	Lung	lung
19	chr6:15642800-15662000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr6:15643000-15662000	Weak transcription	Fetal Stomach	stomach
21	chr6:15644400-15661800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr6:15644400-15662000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr6:15644800-15661800	Weak transcription	HepG2	liver
24	chr6:15644800-15662000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr6:15644800-15662000	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr6:15645600-15661800	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr6:15646000-15662000	Weak transcription	NHDF-Ad	bronchial
28	chr6:15646200-15662000	Weak transcription	Fetal Muscle Trunk	muscle
29	chr6:15647800-15662000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr6:15648200-15662200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr6:15648600-15661000	Weak transcription	Fetal Intestine Large	intestine
32	chr6:15648600-15662000	Weak transcription	Fetal Lung	lung
33	chr6:15648800-15662000	Weak transcription	Fetal Brain Female	brain
34	chr6:15649400-15662000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr6:15649600-15662000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr6:15649800-15662000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr6:15649800-15662000	Weak transcription	Liver	Liver
38	chr6:15649800-15662000	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr6:15649800-15662200	Weak transcription	HSMM	muscle
40	chr6:15650400-15661800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr6:15650800-15662000	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr6:15651000-15659400	Weak transcription	Fetal Intestine Small	intestine
43	chr6:15651000-15662000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr6:15651200-15662000	Weak transcription	Adipose Nuclei	Adipose
45	chr6:15652000-15660800	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr6:15652000-15662000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr6:15654200-15662000	Weak transcription	Right Atrium	heart
48	chr6:15654400-15660800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr6:15654400-15662000	Weak transcription	Fetal Heart	heart
50	chr6:15654800-15660400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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