Variant report

Variant	rs10004910
Chromosome Location	chr4:57968444-57968445
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11133482	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11133483	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11133484	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13108835	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13124681	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13129156	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13147020	0.92[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4075349	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6554428	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6825609	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7661524	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7670481	0.87[AMR][1000 genomes]
rs7681360	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9993153	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10004910	KIT	cis	cerebellum	SCAN
rs10004910	IGFBP7	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57956800-57974400	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr4:57957000-57974600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr4:57957200-57975200	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr4:57958200-57975200	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr4:57958200-57975400	Weak transcription	Small Intestine	intestine
6	chr4:57959800-57973400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr4:57960600-57968600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr4:57961400-57969200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr4:57963800-57969600	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr4:57963800-57969800	Enhancers	Fetal Heart	heart
11	chr4:57963800-57970600	Enhancers	NHDF-Ad	bronchial
12	chr4:57964000-57973200	Weak transcription	Duodenum Mucosa	Duodenum
13	chr4:57964200-57972200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr4:57964600-57973200	Weak transcription	Pancreas	Pancrea
15	chr4:57965000-57968600	Weak transcription	Colonic Mucosa	Colon
16	chr4:57965000-57969200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr4:57965600-57969600	Enhancers	Ovary	ovary
18	chr4:57965600-57972600	Weak transcription	Thymus	Thymus
19	chr4:57965800-57969200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr4:57966000-57969200	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr4:57966200-57975200	Weak transcription	Lung	lung
22	chr4:57966400-57969000	Weak transcription	Fetal Thymus	thymus
23	chr4:57966600-57968800	Weak transcription	Aorta	Aorta
24	chr4:57966600-57969800	Enhancers	Fetal Kidney	kidney
25	chr4:57966800-57969800	Enhancers	Colon Smooth Muscle	Colon
26	chr4:57967000-57968600	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr4:57967000-57968600	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr4:57967000-57969000	Enhancers	Rectal Smooth Muscle	rectum
29	chr4:57967000-57969600	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr4:57967000-57969600	Genic enhancers	HSMMtube	muscle
31	chr4:57967000-57969800	Enhancers	NHLF	lung
32	chr4:57967000-57970200	Enhancers	Fetal Stomach	stomach
33	chr4:57967200-57968800	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr4:57967200-57969000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr4:57967200-57969400	Flanking Active TSS	A549	lung
36	chr4:57967200-57969600	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr4:57967200-57969600	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr4:57967400-57968600	Enhancers	Brain Cingulate Gyrus	brain
39	chr4:57967400-57969200	Enhancers	Adipose Nuclei	Adipose
40	chr4:57967400-57969600	Enhancers	Right Atrium	heart
41	chr4:57967400-57969800	Enhancers	Fetal Lung	lung
42	chr4:57967400-57970600	Enhancers	Fetal Muscle Leg	muscle
43	chr4:57967600-57968600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr4:57967600-57969000	Weak transcription	Spleen	Spleen
45	chr4:57967600-57969600	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr4:57967600-57969600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
47	chr4:57967600-57969800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr4:57967600-57969800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr4:57967600-57970000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr4:57967800-57969000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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