Variant report

Variant	rs7769054
Chromosome Location	chr6:28209197-28209198
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28207533..28210874-chr6:28216267..28219988,4	MCF-7	breast:
2	chr6:28121677..28124555-chr6:28208936..28210698,3	K562	blood:
3	chr6:28206024..28209591-chr6:28211608..28215918,4	MCF-7	breast:
4	chr6:28103041..28105125-chr6:28207182..28210189,3	K562	blood:

Variant related genes	Relation type
ENSG00000269293	Chromatin interaction
ENSG00000261839	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10484404	0.90[CEU][hapmap]
rs1150697	0.81[CEU][hapmap]
rs1150698	0.88[EUR][1000 genomes]
rs1150699	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1150704	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1150714	0.80[CEU][hapmap]
rs11751702	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11752073	0.90[CEU][hapmap]
rs11756111	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11757730	0.86[ASN][1000 genomes]
rs11758148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11758337	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11970439	1.00[JPT][hapmap]
rs1233664	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1233665	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1233666	1.00[CEU][hapmap]
rs1474589	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs16893817	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16893937	0.80[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs16901846	0.80[CEU][hapmap]
rs17301128	1.00[JPT][hapmap]
rs1736890	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs1736894	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs1736904	0.81[YRI][hapmap]
rs17776284	1.00[JPT][hapmap]
rs1778469	0.87[EUR][1000 genomes]
rs1890809	0.90[CEU][hapmap]
rs2185955	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2232422	0.80[CEU][hapmap]
rs2235358	1.00[JPT][hapmap]
rs2235359	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2281043	0.80[CEU][hapmap]
rs2299031	1.00[JPT][hapmap]
rs2622315	0.90[CEU][hapmap]
rs3800325	0.80[CEU][hapmap]
rs3800326	1.00[JPT][hapmap]
rs55831267	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6456811	0.80[CEU][hapmap]
rs6903652	1.00[JPT][hapmap]
rs6903823	0.88[JPT][hapmap]
rs6905368	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6912584	1.00[JPT][hapmap]
rs6917759	0.90[CEU][hapmap]
rs6921919	1.00[JPT][hapmap]
rs6922111	1.00[JPT][hapmap]
rs6923170	0.80[CEU][hapmap]
rs6929559	0.90[CEU][hapmap]
rs73740584	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73740587	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7741443	0.86[ASN][1000 genomes]
rs7744788	0.80[CEU][hapmap]
rs993619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]

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	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7769054	AL022393.7	cis	Thyroid	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28193600-28213400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr6:28193800-28211800	Weak transcription	Fetal Thymus	thymus
3	chr6:28193800-28218400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr6:28193800-28218400	Weak transcription	Stomach Mucosa	stomach
5	chr6:28194000-28211000	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr6:28194000-28211800	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr6:28194000-28212800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr6:28194000-28213000	Weak transcription	Thymus	Thymus
9	chr6:28194000-28213600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr6:28196800-28212400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr6:28196800-28212400	Weak transcription	Small Intestine	intestine
12	chr6:28196800-28213600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr6:28197000-28212400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr6:28198800-28212200	Weak transcription	Hela-S3	cervix
15	chr6:28199200-28213200	Weak transcription	Colonic Mucosa	Colon
16	chr6:28199800-28213600	Weak transcription	NHDF-Ad	bronchial
17	chr6:28200400-28212400	Weak transcription	Fetal Intestine Small	intestine
18	chr6:28200400-28212600	Weak transcription	NHEK	skin
19	chr6:28200800-28212400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr6:28200800-28212600	Weak transcription	Fetal Heart	heart
21	chr6:28201000-28211000	Weak transcription	Brain Hippocampus Middle	brain
22	chr6:28201000-28211600	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr6:28201000-28212200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr6:28201000-28212200	Weak transcription	Brain Anterior Caudate	brain
25	chr6:28201000-28212400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr6:28201000-28212400	Weak transcription	HMEC	breast
27	chr6:28201000-28212800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr6:28201000-28212800	Weak transcription	Pancreas	Pancrea
29	chr6:28201000-28212800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr6:28201000-28212800	Weak transcription	Right Ventricle	heart
31	chr6:28201200-28212200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr6:28201600-28211600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr6:28201600-28211800	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr6:28201600-28212000	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr6:28201600-28212400	Weak transcription	Esophagus	oesophagus
36	chr6:28201600-28212600	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr6:28201600-28212600	Weak transcription	Brain Angular Gyrus	brain
38	chr6:28201600-28212600	Weak transcription	Fetal Brain Male	brain
39	chr6:28201600-28212800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr6:28201600-28212800	Weak transcription	Gastric	stomach
41	chr6:28201600-28213000	Weak transcription	HepG2	liver
42	chr6:28201600-28213400	Weak transcription	Fetal Kidney	kidney
43	chr6:28201600-28219400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr6:28201800-28211000	Weak transcription	Psoas Muscle	Psoas
45	chr6:28201800-28211800	Weak transcription	Osteobl	bone
46	chr6:28201800-28212000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr6:28202000-28211400	Weak transcription	Primary B cells from peripheral blood	blood
48	chr6:28202000-28211600	Weak transcription	Stomach Smooth Muscle	stomach
49	chr6:28202000-28211800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr6:28202000-28212000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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