Variant report

Variant	rs12135769
Chromosome Location	chr1:185257061-185257062
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:185256584..185258275-chr1:185263468..185265157,2	K562	blood:
2	chr1:185256781..185259746-chr1:185259822..185261591,2	K562	blood:
3	chr1:185255885..185258419-chr1:185280171..185282266,2	K562	blood:
4	chr1:185256179..185258931-chr1:185354398..185356774,2	K562	blood:
5	chr1:185256550..185258256-chr1:185284838..185287502,2	MCF-7	breast:
6	chr1:185255623..185257727-chr1:185264157..185265832,2	MCF-7	breast:
7	chr1:185256140..185258488-chr1:185259752..185262450,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000273004	Chromatin interaction
ENSG00000116679	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10174	0.89[CEU][hapmap];0.84[TSI][hapmap]
rs10218496	0.83[ASN][1000 genomes]
rs10798002	0.86[EUR][1000 genomes]
rs10798003	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10798004	0.84[ASW][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];0.88[TSI][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10798006	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10911700	0.92[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10911702	0.89[CEU][hapmap];0.82[TSI][hapmap]
rs10911704	0.85[CEU][hapmap]
rs10911706	0.81[ASN][1000 genomes]
rs10911707	0.82[TSI][hapmap]
rs12026391	0.89[CEU][hapmap];0.84[TSI][hapmap]
rs12041704	0.96[CEU][hapmap];0.89[TSI][hapmap];0.92[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]
rs12136040	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1336753	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1889976	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2095610	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2295212	0.81[ASN][1000 genomes]
rs2378909	0.82[EUR][1000 genomes]
rs2378910	0.96[CEU][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs2383269	0.84[ASN][1000 genomes]
rs34611062	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57977436	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[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	0.82[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6685627	0.86[EUR][1000 genomes]
rs7123	0.84[TSI][hapmap]
rs726567	0.85[CEU][hapmap]
rs7537341	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]
rs7539575	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[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	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7550599	0.83[ASN][1000 genomes]
rs7553819	0.81[ASN][1000 genomes]
rs883753	0.96[CEU][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.86[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12135769	IVNS1ABP	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:91 , 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	chr1:185235400-185265400	Weak transcription	Brain Substantia Nigra	brain
7	chr1:185236600-185265600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:185239600-185262000	Weak transcription	HSMMtube	muscle
9	chr1:185239800-185262000	Weak transcription	Fetal Muscle Leg	muscle
10	chr1:185239800-185263800	Weak transcription	Brain Anterior Caudate	brain
11	chr1:185240000-185265800	Weak transcription	Fetal Lung	lung
12	chr1:185240200-185267200	Weak transcription	Gastric	stomach
13	chr1:185240400-185268800	Weak transcription	Aorta	Aorta
14	chr1:185240800-185273000	Weak transcription	Spleen	Spleen
15	chr1:185241600-185261800	Weak transcription	Fetal Brain Female	brain
16	chr1:185242000-185262000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:185244000-185261400	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr1:185244800-185264800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:185245400-185268800	Weak transcription	Esophagus	oesophagus
20	chr1:185245600-185261000	Weak transcription	Fetal Intestine Large	intestine
21	chr1:185245800-185261600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr1:185245800-185268400	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr1:185245800-185273000	Weak transcription	Right Ventricle	heart
24	chr1:185246200-185261600	Weak transcription	Lung	lung
25	chr1:185246800-185265600	Weak transcription	NHLF	lung
26	chr1:185247600-185267800	Weak transcription	Fetal Stomach	stomach
27	chr1:185248000-185260800	Weak transcription	Primary B cells from cord blood	blood
28	chr1:185248000-185261800	Weak transcription	Brain Angular Gyrus	brain
29	chr1:185248200-185266800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr1:185248800-185265200	Weak transcription	Rectal Smooth Muscle	rectum
31	chr1:185249000-185263400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:185249200-185262600	Weak transcription	Osteobl	bone
33	chr1:185249200-185263000	Weak transcription	Brain Hippocampus Middle	brain
34	chr1:185249200-185265800	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr1:185250200-185260200	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr1:185250200-185264000	Weak transcription	Colon Smooth Muscle	Colon
37	chr1:185250200-185265400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr1:185250400-185265600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr1:185250600-185263000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr1:185250600-185263800	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr1:185250800-185258600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr1:185250800-185259800	Weak transcription	Primary hematopoietic stem cells	blood
43	chr1:185250800-185261800	Weak transcription	Right Atrium	heart
44	chr1:185251200-185263200	Weak transcription	Liver	Liver
45	chr1:185251200-185263200	Weak transcription	Dnd41	blood
46	chr1:185251200-185263600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr1:185251200-185263600	Weak transcription	A549	lung
48	chr1:185251200-185264400	Weak transcription	Fetal Muscle Trunk	muscle
49	chr1:185251200-185265600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr1:185251200-185266400	Weak transcription	Stomach Smooth Muscle	stomach

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