Variant report

Variant	rs7774887
Chromosome Location	chr6:149344340-149344341
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:149335195..149337795-chr6:149343011..149345785,3	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10457074	0.95[CEU][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1317171	0.86[CEU][hapmap]
rs1934224	0.91[CEU][hapmap];0.82[CHD][hapmap];0.83[JPT][hapmap];0.83[TSI][hapmap]
rs2275423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2340751	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2340752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2340798	0.86[CEU][hapmap]
rs2340801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2340802	0.95[CEU][hapmap];0.83[CHB][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2879843	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4318907	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4377808	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4897074	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4897076	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6570920	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6904550	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6911303	0.87[JPT][hapmap]
rs6915298	0.86[CEU][hapmap]
rs6930989	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6931675	0.86[CEU][hapmap];0.87[GIH][hapmap]
rs6931744	0.95[CEU][hapmap];0.83[CHB][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6936176	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7738162	0.82[CEU][hapmap]
rs7747463	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7748978	1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7765778	0.90[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7774457	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7776117	0.86[CEU][hapmap]
rs9285516	0.82[CEU][hapmap]
rs9377187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9377188	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]
rs9399678	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7774887	C6orf97	cis	cerebellum	SCAN
rs7774887	SUMO4	cis	cerebellum	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149305400-149381400	Weak transcription	Gastric	stomach
2	chr6:149320200-149344800	Weak transcription	Left Ventricle	heart
3	chr6:149321800-149349800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr6:149327200-149353000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:149334000-149353400	Weak transcription	Spleen	Spleen
6	chr6:149334400-149352800	Weak transcription	HSMMtube	muscle
7	chr6:149336000-149345200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:149336200-149344400	Weak transcription	Fetal Intestine Small	intestine
9	chr6:149336200-149345200	Weak transcription	Right Atrium	heart
10	chr6:149336200-149349800	Weak transcription	Brain Anterior Caudate	brain
11	chr6:149336200-149351400	Weak transcription	Fetal Thymus	thymus
12	chr6:149336200-149353000	Weak transcription	Pancreas	Pancrea
13	chr6:149336200-149353200	Weak transcription	Esophagus	oesophagus
14	chr6:149336200-149358000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:149336400-149347600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr6:149336400-149354000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr6:149336600-149347400	Weak transcription	Adipose Nuclei	Adipose
18	chr6:149336800-149353200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr6:149337200-149344800	Weak transcription	Fetal Heart	heart
20	chr6:149337200-149347400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr6:149337200-149353600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr6:149337600-149347200	Weak transcription	Osteobl	bone
23	chr6:149337600-149347400	Weak transcription	NH-A	brain
24	chr6:149337600-149352800	Weak transcription	NHLF	lung
25	chr6:149337600-149353000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr6:149337600-149358000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr6:149338200-149351800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr6:149338200-149352400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr6:149338800-149350000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr6:149339200-149347000	Weak transcription	Fetal Intestine Large	intestine
31	chr6:149339400-149353200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr6:149339400-149364600	Weak transcription	Lung	lung
33	chr6:149339800-149353200	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr6:149340000-149344600	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr6:149340000-149345400	Strong transcription	Fetal Stomach	stomach
36	chr6:149340000-149346000	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr6:149340000-149347600	Weak transcription	Duodenum Mucosa	Duodenum
38	chr6:149340200-149345400	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr6:149340200-149345400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr6:149340200-149345600	Strong transcription	Ovary	ovary
41	chr6:149340200-149345800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr6:149340200-149345800	Strong transcription	Primary B cells from peripheral blood	blood
43	chr6:149340400-149344800	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr6:149340400-149345000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr6:149340400-149345600	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr6:149340400-149345800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr6:149340600-149344600	Strong transcription	Primary B cells from cord blood	blood
48	chr6:149340600-149344800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr6:149340800-149345200	Strong transcription	Colon Smooth Muscle	Colon
50	chr6:149340800-149345600	Strong transcription	H1 Cell Line	embryonic stem cell

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