Variant report

Variant	rs7994305
Chromosome Location	chr13:110868460-110868461
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10492498	1.00[JPT][hapmap]
rs12867220	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs12868203	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs12868210	0.85[EUR][1000 genomes]
rs12869358	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs12869391	0.85[EUR][1000 genomes]
rs12874407	1.00[JPT][hapmap]
rs1373749	1.00[JPT][hapmap]
rs1982315	1.00[JPT][hapmap]
rs4773131	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs490727	1.00[JPT][hapmap]
rs61964980	0.86[EUR][1000 genomes]
rs685884	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs686746	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs7331702	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs7332235	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs7333008	0.85[EUR][1000 genomes]
rs7996925	1.00[JPT][hapmap]
rs9515163	1.00[JPT][hapmap]
rs9515165	1.00[JPT][hapmap]
rs9515166	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs9521642	1.00[JPT][hapmap]
rs9521644	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs9521649	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs9583467	0.86[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs9588117	0.86[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs995223	1.00[JPT][hapmap]

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	nsv1052147	chr13:110765635-110917782	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv1182	chr13:110829691-110875029	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv1038914	chr13:110860219-111190104	Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7994305	COL4A1	cis	parietal	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:110827600-110869000	Weak transcription	Brain Hippocampus Middle	brain
2	chr13:110829600-110874400	Weak transcription	A549	lung
3	chr13:110829800-110869600	Weak transcription	Small Intestine	intestine
4	chr13:110830000-110870800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr13:110830200-110869600	Weak transcription	Fetal Brain Male	brain
6	chr13:110836400-110874200	Weak transcription	Esophagus	oesophagus
7	chr13:110840800-110870200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr13:110846400-110869000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr13:110846400-110879800	Weak transcription	Pancreas	Pancrea
10	chr13:110852000-110869800	Weak transcription	Brain Germinal Matrix	brain
11	chr13:110853600-110879800	Weak transcription	Gastric	stomach
12	chr13:110861400-110870800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr13:110862800-110869600	Weak transcription	HMEC	breast
14	chr13:110863800-110868600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr13:110863800-110869200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr13:110865200-110871400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr13:110865400-110868600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr13:110865400-110869000	Weak transcription	Liver	Liver
19	chr13:110865400-110874400	Weak transcription	Colonic Mucosa	Colon
20	chr13:110865600-110868800	Weak transcription	Fetal Kidney	kidney
21	chr13:110866000-110873400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr13:110866200-110868600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr13:110866200-110874000	Weak transcription	NHEK	skin
24	chr13:110866200-110882400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr13:110866400-110871000	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr13:110866400-110885000	Weak transcription	Fetal Intestine Large	intestine
27	chr13:110866600-110871000	Enhancers	Left Ventricle	heart
28	chr13:110866600-110874200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr13:110866600-110874200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr13:110866600-110874400	Weak transcription	Fetal Intestine Small	intestine
31	chr13:110866800-110870000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr13:110866800-110870000	Enhancers	Right Ventricle	heart
33	chr13:110866800-110871400	Enhancers	Colon Smooth Muscle	Colon
34	chr13:110867000-110871800	Enhancers	Fetal Lung	lung
35	chr13:110867200-110869600	Weak transcription	Spleen	Spleen
36	chr13:110867200-110871000	Enhancers	Adipose Nuclei	Adipose
37	chr13:110867200-110871600	Enhancers	Rectal Smooth Muscle	rectum
38	chr13:110867200-110871800	Enhancers	Fetal Muscle Leg	muscle
39	chr13:110867400-110870000	Enhancers	Fetal Stomach	stomach
40	chr13:110867800-110870600	Weak transcription	Fetal Muscle Trunk	muscle
41	chr13:110867800-110870800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr13:110868000-110868600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr13:110868000-110868800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr13:110868000-110869000	Enhancers	Osteobl	bone
45	chr13:110868000-110869800	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr13:110868000-110870000	Enhancers	Duodenum Mucosa	Duodenum
47	chr13:110868000-110870200	Enhancers	Muscle Satellite Cultured Cells	--
48	chr13:110868000-110871200	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr13:110868000-110871400	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr13:110868000-110871600	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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