Variant report

Variant	rs9377188
Chromosome Location	chr6:149351381-149351382
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:149351101..149353287-chr6:149403711..149405332,2	MCF-7	breast:
2	chr6:149349493..149352032-chr6:149352609..149354718,2	K562	blood:
3	chr6:149350211..149352689-chr6:149414804..149416948,2	MCF-7	breast:
4	chr6:149349779..149353985-chr6:149637379..149639962,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000055208	Chromatin interaction
ENSG00000236591	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10457074	0.81[CEU][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1317171	0.92[MEX][hapmap];0.80[AMR][1000 genomes]
rs2275423	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2340751	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2340752	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2340801	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2340802	0.83[CHB][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2486409	0.85[CEU][hapmap]
rs2486411	0.89[CEU][hapmap]
rs2500549	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2879843	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4318907	1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4377808	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4897074	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4897076	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6570920	1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6904550	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6911303	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs6915298	0.92[MEX][hapmap]
rs6930989	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6931675	0.86[GIH][hapmap];0.88[MEX][hapmap]
rs6931744	0.83[CHB][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6935330	0.92[MEX][hapmap]
rs6936176	0.81[CEU][hapmap];0.81[AMR][1000 genomes]
rs7747463	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7748978	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7761119	0.87[MEX][hapmap]
rs7765778	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7774457	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7774887	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7776117	0.80[AMR][1000 genomes]
rs9285516	0.92[MEX][hapmap]
rs9377187	1.00[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9399678	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032690	chr6:149206106-149398712	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1032319	chr6:149271433-149550525	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv538470	chr6:149271433-149550525	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv830842	chr6:149272321-149427340	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	esv3450509	chr6:149349709-149351657	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	esv3370887	chr6:149350866-149352052	Enhancers Weak transcription Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	esv3475165	chr6:149350872-149351991	Weak transcription Enhancers Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	esv3475166	chr6:149350872-149351991	Weak transcription Enhancers Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9377188	C6orf97	cis	cerebellum	SCAN
rs9377188	SUMO4	cis	cerebellum	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149305400-149381400	Weak transcription	Gastric	stomach
2	chr6:149327200-149353000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr6:149334000-149353400	Weak transcription	Spleen	Spleen
4	chr6:149334400-149352800	Weak transcription	HSMMtube	muscle
5	chr6:149336200-149351400	Weak transcription	Fetal Thymus	thymus
6	chr6:149336200-149353000	Weak transcription	Pancreas	Pancrea
7	chr6:149336200-149353200	Weak transcription	Esophagus	oesophagus
8	chr6:149336200-149358000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:149336400-149354000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr6:149336800-149353200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr6:149337200-149353600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr6:149337600-149352800	Weak transcription	NHLF	lung
13	chr6:149337600-149353000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:149337600-149358000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr6:149338200-149351800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr6:149338200-149352400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr6:149339400-149353200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr6:149339400-149364600	Weak transcription	Lung	lung
19	chr6:149339800-149353200	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr6:149341000-149353400	Weak transcription	Aorta	Aorta
21	chr6:149341000-149365400	Weak transcription	Right Ventricle	heart
22	chr6:149341200-149352200	Weak transcription	Primary T cells from cord blood	blood
23	chr6:149341400-149353200	Weak transcription	Brain Hippocampus Middle	brain
24	chr6:149342400-149353400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr6:149343000-149352800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr6:149343200-149352400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr6:149343200-149358000	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr6:149344000-149352000	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr6:149344000-149352800	Weak transcription	Fetal Lung	lung
30	chr6:149344000-149353000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr6:149344000-149357200	Weak transcription	Fetal Muscle Trunk	muscle
32	chr6:149344000-149357400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr6:149344600-149353400	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr6:149344600-149353600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr6:149344600-149353800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr6:149344600-149357800	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr6:149344800-149354800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr6:149344800-149358000	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr6:149345000-149352800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr6:149345000-149353000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr6:149345000-149355200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr6:149345400-149353000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr6:149345400-149353000	Weak transcription	Fetal Stomach	stomach
44	chr6:149345400-149353600	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr6:149345400-149362000	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr6:149345600-149353000	Weak transcription	Ovary	ovary
47	chr6:149345600-149355000	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr6:149345600-149358000	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr6:149345800-149352000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr6:149345800-149352600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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