Variant report

Variant	rs1949840
Chromosome Location	chr7:12747045-12747046
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:12746516..12748065-chr7:12787286..12789975,2	K562	blood:
2	chr7:12724561..12731097-chr7:12744483..12748724,8	K562	blood:
3	chr7:12736363..12739196-chr7:12746914..12748860,2	K562	blood:

Variant related genes	Relation type
ENSG00000122644	Chromatin interaction
ENSG00000271253	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs10278922	0.83[EUR][1000 genomes]
rs2217801	0.80[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6970019	0.80[CEU][hapmap];0.87[GIH][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024554	chr7:12214722-12967418	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv538735	chr7:12214722-12967418	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers 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	58 gene(s)	inside rSNPs	diseases
3	nsv830907	chr7:12661239-12818250	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv932020	chr7:12676890-13239551	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv830908	chr7:12695007-12870475	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	esv1794967	chr7:12710385-12758624	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	n/a
7	nsv868830	chr7:12712753-13517417	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
8	esv2762652	chr7:12733802-12749636	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
9	esv2422346	chr7:12739291-12883550	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1027501	chr7:12743592-12927109	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1949840	IGDCC4	trans	lymphoblastoid	seeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:12744200-12749000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr7:12745200-12748400	Enhancers	Hela-S3	cervix
3	chr7:12745200-12750600	Enhancers	HMEC	breast
4	chr7:12745200-12750800	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr7:12745400-12747600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr7:12745400-12750200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr7:12745800-12747200	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr7:12745800-12747400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr7:12745800-12747600	Enhancers	Osteobl	bone
10	chr7:12745800-12750200	Enhancers	NHEK	skin
11	chr7:12746000-12747600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr7:12746200-12747200	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr7:12746200-12747600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr7:12746200-12747600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr7:12746200-12747600	Flanking Active TSS	A549	lung
16	chr7:12746200-12748200	Enhancers	K562	blood
17	chr7:12746400-12747200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr7:12746400-12747400	Enhancers	Stomach Mucosa	stomach
19	chr7:12746400-12747400	Enhancers	NHDF-Ad	bronchial
20	chr7:12746400-12747600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr7:12746400-12747800	Enhancers	HSMM	muscle
22	chr7:12746400-12750200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr7:12746600-12747200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr7:12746600-12747400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr7:12746600-12747600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr7:12746600-12747600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr7:12746800-12747800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
28	chr7:12746800-12755000	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr7:12747000-12747200	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr7:12747000-12747400	Weak transcription	HSMMtube	muscle
31	chr7:12747000-12748800	Weak transcription	Placenta	Placenta
32	chr7:12747000-12749000	Weak transcription	Fetal Intestine Small	intestine
33	chr7:12747000-12750000	Weak transcription	Fetal Kidney	kidney
34	chr7:12747000-12752000	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr7:12747000-12753200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr7:12747000-12753400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr7:12747000-12755000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr7:12747000-12755000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr7:12747000-12755000	Weak transcription	NH-A	brain

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