Variant report

Variant	rs6657944
Chromosome Location	chr1:220951135-220951136
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:220950664..220952187-chr1:220959434..220961984,2	MCF-7	breast:
2	chr1:220949362..220952118-chr1:220955104..220958049,2	K562	blood:

Variant related genes	Relation type
ENSG00000186205	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10779415	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs10863562	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs11118597	0.81[ASW][hapmap];0.83[CEU][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11118599	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11118600	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12027850	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12402066	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12562235	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12568838	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17008609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2642424	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs337147	0.83[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs337148	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs337150	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs365398	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3795536	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs381023	0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs421736	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs425473	0.83[CEU][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4846662	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6659604	0.82[EUR][1000 genomes]
rs6697965	0.88[ASW][hapmap];1.00[CEU][hapmap];0.81[JPT][hapmap];0.92[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7518916	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7519399	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7519414	1.00[CEU][hapmap];0.86[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7536276	1.00[CEU][hapmap];0.83[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7539769	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7542648	1.00[CEU][hapmap];0.86[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7542723	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7553948	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7556458	1.00[CEU][hapmap];0.81[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7556561	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9430990	0.83[CEU][hapmap]

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	nsv523389	chr1:220926844-220956012	Genic enhancers Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6657944	C1orf115	Cis_1M	lymphoblastoid	RTeQTL
rs6657944	MOSC2	Cis_1M	lymphoblastoid	RTeQTL
rs6657944	C1orf115	cis	Nerve Tibial	GTEx

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220922800-220959600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:220922800-220959600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:220925000-220959400	Weak transcription	Brain Angular Gyrus	brain
4	chr1:220930000-220959600	Weak transcription	Psoas Muscle	Psoas
5	chr1:220930400-220959600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:220931200-220959000	Weak transcription	Brain Substantia Nigra	brain
7	chr1:220936200-220959600	Weak transcription	A549	lung
8	chr1:220936600-220958200	Weak transcription	Esophagus	oesophagus
9	chr1:220939000-220960400	Weak transcription	Small Intestine	intestine
10	chr1:220943000-220958400	Weak transcription	HepG2	liver
11	chr1:220943000-220959000	Strong transcription	Fetal Intestine Large	intestine
12	chr1:220944200-220956000	Weak transcription	Pancreas	Pancrea
13	chr1:220944200-220959200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:220944200-220959400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:220944200-220959400	Weak transcription	Fetal Kidney	kidney
16	chr1:220944200-220959600	Weak transcription	NHLF	lung
17	chr1:220944200-220959800	Weak transcription	Gastric	stomach
18	chr1:220944400-220954600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr1:220944400-220956000	Weak transcription	Aorta	Aorta
20	chr1:220944400-220956800	Weak transcription	Spleen	Spleen
21	chr1:220944400-220958800	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr1:220944400-220959000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr1:220944400-220959200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr1:220944400-220959400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr1:220944400-220959400	Weak transcription	Colonic Mucosa	Colon
26	chr1:220944400-220959400	Weak transcription	Right Ventricle	heart
27	chr1:220945000-220951800	Weak transcription	Ovary	ovary
28	chr1:220945600-220953200	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr1:220945800-220959200	Weak transcription	Colon Smooth Muscle	Colon
30	chr1:220946000-220956800	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr1:220946200-220951600	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr1:220946400-220953400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr1:220946400-220956200	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr1:220946600-220958600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:220946800-220958800	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr1:220947800-220952600	Weak transcription	Stomach Smooth Muscle	stomach
37	chr1:220948400-220951600	Weak transcription	Left Ventricle	heart
38	chr1:220948400-220953200	Weak transcription	Adipose Nuclei	Adipose
39	chr1:220949800-220954200	Strong transcription	Fetal Intestine Small	intestine
40	chr1:220950000-220951200	Strong transcription	Hela-S3	cervix
41	chr1:220950000-220951400	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr1:220950000-220953600	Strong transcription	Fetal Muscle Leg	muscle
43	chr1:220950200-220957800	Strong transcription	Duodenum Mucosa	Duodenum
44	chr1:220950200-220959200	Weak transcription	Brain Cingulate Gyrus	brain
45	chr1:220950400-220951200	Strong transcription	Fetal Lung	lung
46	chr1:220950400-220952200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
47	chr1:220950400-220953000	Enhancers	Primary B cells from cord blood	blood
48	chr1:220950400-220953800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr1:220950400-220958000	Strong transcription	Fetal Muscle Trunk	muscle
50	chr1:220950400-220959400	Weak transcription	Brain Inferior Temporal Lobe	brain

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