Variant report

Variant	rs7537341
Chromosome Location	chr1:185253790-185253791
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:185249006..185250528-chr1:185252328..185254308,2	K562	blood:
2	chr1:185252488..185254070-chr1:185283476..185284989,2	MCF-7	breast:
3	chr1:185251775..185256008-chr1:185261295..185263374,3	K562	blood:
4	chr1:185238608..185240468-chr1:185252682..185255068,2	K562	blood:
5	chr1:185253508..185256356-chr1:185274825..185277482,3	K562	blood:
6	chr1:185252978..185255340-chr1:185264252..185266302,2	K562	blood:
7	chr1:185248836..185252161-chr1:185252786..185255839,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000238061	Chromatin interaction
ENSG00000116679	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10174	0.82[CEU][hapmap];0.85[TSI][hapmap]
rs10218496	0.83[ASN][1000 genomes]
rs10798002	0.81[EUR][1000 genomes]
rs10798003	0.91[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10798004	1.00[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10798006	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10911700	0.83[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10911702	0.82[CEU][hapmap];0.83[TSI][hapmap]
rs10911706	0.81[ASN][1000 genomes]
rs10911707	0.82[TSI][hapmap]
rs12026391	0.82[CEU][hapmap];0.83[TSI][hapmap]
rs12041704	0.89[CEU][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs12096987	0.87[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs12119471	0.85[ASN][1000 genomes]
rs12127840	0.85[ASN][1000 genomes]
rs12135172	0.87[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs12135769	0.91[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12136040	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1336753	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1889976	0.83[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2095610	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2295212	0.81[ASN][1000 genomes]
rs2378910	0.89[CEU][hapmap];0.88[MEX][hapmap];0.81[EUR][1000 genomes]
rs2383269	0.84[ASN][1000 genomes]
rs34611062	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57977436	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6424975	0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6666742	0.87[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs6682891	0.81[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6685627	0.81[EUR][1000 genomes]
rs6687774	0.80[TSI][hapmap]
rs7123	0.82[TSI][hapmap]
rs7539575	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7539658	0.87[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs7542721	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7550599	0.83[ASN][1000 genomes]
rs7553819	0.81[ASN][1000 genomes]
rs883753	0.89[CEU][hapmap];0.88[MEX][hapmap];0.81[EUR][1000 genomes]
rs9988622	0.81[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	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv548398	chr1:185136458-186003094	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7537341	RP4-635A23.4	cis	Artery Tibial	GTEx
rs7537341	NCRNA00272	cis	parietal	SCAN
rs7537341	IVNS1ABP	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:185193800-185263600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr1:185218800-185269400	Weak transcription	Pancreas	Pancrea
3	chr1:185227800-185262000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:185231000-185263400	Weak transcription	Fetal Kidney	kidney
5	chr1:185235000-185261800	Weak transcription	Duodenum Mucosa	Duodenum
6	chr1:185235200-185256800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr1:185235400-185265400	Weak transcription	Brain Substantia Nigra	brain
8	chr1:185236600-185265600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:185239600-185262000	Weak transcription	HSMMtube	muscle
10	chr1:185239800-185262000	Weak transcription	Fetal Muscle Leg	muscle
11	chr1:185239800-185263800	Weak transcription	Brain Anterior Caudate	brain
12	chr1:185240000-185265800	Weak transcription	Fetal Lung	lung
13	chr1:185240200-185267200	Weak transcription	Gastric	stomach
14	chr1:185240400-185268800	Weak transcription	Aorta	Aorta
15	chr1:185240800-185273000	Weak transcription	Spleen	Spleen
16	chr1:185241600-185261800	Weak transcription	Fetal Brain Female	brain
17	chr1:185242000-185262000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:185244000-185261400	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr1:185244800-185264800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:185245400-185268800	Weak transcription	Esophagus	oesophagus
21	chr1:185245600-185261000	Weak transcription	Fetal Intestine Large	intestine
22	chr1:185245800-185261600	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr1:185245800-185268400	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr1:185245800-185273000	Weak transcription	Right Ventricle	heart
25	chr1:185246000-185254000	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr1:185246200-185261600	Weak transcription	Lung	lung
27	chr1:185246800-185265600	Weak transcription	NHLF	lung
28	chr1:185247400-185253800	Weak transcription	Fetal Intestine Small	intestine
29	chr1:185247600-185267800	Weak transcription	Fetal Stomach	stomach
30	chr1:185247800-185256600	Weak transcription	Ovary	ovary
31	chr1:185248000-185260800	Weak transcription	Primary B cells from cord blood	blood
32	chr1:185248000-185261800	Weak transcription	Brain Angular Gyrus	brain
33	chr1:185248200-185266800	Weak transcription	Brain Cingulate Gyrus	brain
34	chr1:185248800-185254600	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr1:185248800-185265200	Weak transcription	Rectal Smooth Muscle	rectum
36	chr1:185249000-185263400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:185249200-185262600	Weak transcription	Osteobl	bone
38	chr1:185249200-185263000	Weak transcription	Brain Hippocampus Middle	brain
39	chr1:185249200-185265800	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr1:185249600-185254400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr1:185250000-185254600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr1:185250200-185260200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr1:185250200-185264000	Weak transcription	Colon Smooth Muscle	Colon
44	chr1:185250200-185265400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr1:185250400-185265600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr1:185250600-185255200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr1:185250600-185263000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:185250600-185263800	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr1:185250800-185253800	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr1:185250800-185254000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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