Variant report

Variant	rs6434028
Chromosome Location	chr2:153287902-153287903
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10184210	0.90[JPT][hapmap]
rs11898429	0.89[GIH][hapmap];0.90[JPT][hapmap]
rs12614465	0.91[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs16831066	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16831125	0.82[JPT][hapmap]
rs2346201	0.81[JPT][hapmap]
rs2346202	0.90[JPT][hapmap]
rs3811575	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3901192	0.90[JPT][hapmap]
rs4371310	0.86[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4664579	0.81[JPT][hapmap]
rs4664583	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59348655	0.80[EUR][1000 genomes]
rs6721741	0.94[JPT][hapmap]
rs6724305	0.91[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs6729611	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6736856	0.95[JPT][hapmap]
rs7586834	0.81[CHD][hapmap]
rs7600624	0.81[CHD][hapmap]
rs7607429	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9677373	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834419	chr2:153179420-153381476	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	esv3693436	chr2:153219836-153479857	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv875291	chr2:153251742-153339823	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1013777	chr2:153273637-153538546	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6434028	GALNT13	cis	parietal	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153264200-153288200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr2:153272800-153288200	Weak transcription	Right Atrium	heart
3	chr2:153278400-153289800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr2:153278600-153288000	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr2:153278800-153288200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:153278800-153290600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr2:153278800-153291200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr2:153279200-153288200	Weak transcription	Left Ventricle	heart
9	chr2:153279400-153288200	Weak transcription	Placenta	Placenta
10	chr2:153279400-153288200	Weak transcription	Lung	lung
11	chr2:153280000-153305200	Enhancers	Brain Cingulate Gyrus	brain
12	chr2:153280800-153288400	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr2:153281600-153291600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:153282600-153304400	Enhancers	Brain Anterior Caudate	brain
15	chr2:153283000-153288200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr2:153283200-153288200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr2:153283200-153288200	Weak transcription	Fetal Muscle Leg	muscle
18	chr2:153283200-153288800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr2:153283400-153288400	Weak transcription	NHLF	lung
20	chr2:153283400-153288800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr2:153283600-153288600	Weak transcription	HSMMtube	muscle
22	chr2:153283600-153288600	Weak transcription	NH-A	brain
23	chr2:153283600-153288800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr2:153283600-153288800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr2:153283600-153289400	Weak transcription	Pancreas	Pancrea
26	chr2:153283800-153288000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr2:153283800-153288000	Weak transcription	Osteobl	bone
28	chr2:153284200-153291600	Enhancers	Brain Angular Gyrus	brain
29	chr2:153284800-153288000	Weak transcription	HMEC	breast
30	chr2:153285000-153288000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr2:153285000-153290800	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr2:153285400-153289000	Weak transcription	Duodenum Mucosa	Duodenum
33	chr2:153285600-153290000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr2:153285800-153288200	Weak transcription	Ovary	ovary
35	chr2:153285800-153289200	Enhancers	Fetal Kidney	kidney
36	chr2:153285800-153292200	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr2:153286000-153288200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr2:153286000-153289200	Weak transcription	Psoas Muscle	Psoas
39	chr2:153286200-153288200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr2:153286200-153288800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr2:153286200-153290200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr2:153286200-153291600	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr2:153286200-153301000	Enhancers	Brain Hippocampus Middle	brain
44	chr2:153286400-153288200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr2:153286400-153288200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr2:153286400-153288800	Weak transcription	Fetal Lung	lung
47	chr2:153286400-153289400	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr2:153286400-153291800	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr2:153286400-153305200	Enhancers	Brain Substantia Nigra	brain
50	chr2:153286600-153288000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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