Variant report

Variant	rs13108940
Chromosome Location	chr4:99442489-99442490
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:99441293..99445376-chr4:99447706..99451023,3	K562	blood:
2	chr4:99413602..99415848-chr4:99442433..99444375,2	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10002696	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10004753	0.81[CHB][hapmap]
rs10005781	0.82[CHB][hapmap]
rs10006366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10006430	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10018825	0.92[CEU][hapmap];0.90[CHB][hapmap]
rs10021296	0.96[CEU][hapmap];0.90[CHB][hapmap]
rs10025051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11097619	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13116201	0.81[CHB][hapmap]
rs13123700	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13141997	0.88[CEU][hapmap]
rs13149070	0.96[CEU][hapmap];0.90[CHB][hapmap]
rs1528547	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1534555	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs1573478	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap]
rs1919210	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1919211	0.81[CEU][hapmap]
rs2037832	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2866016	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs2866017	0.92[CEU][hapmap];0.90[CHB][hapmap]
rs28886705	0.84[ASN][1000 genomes]
rs4447870	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4699343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4699344	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4699345	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4699348	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4699349	0.92[CEU][hapmap];0.94[JPT][hapmap]
rs4699354	0.94[JPT][hapmap]
rs4699639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4699640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4699644	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4699646	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4699648	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6532742	0.92[CEU][hapmap]
rs6532751	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs6815038	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6823547	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6831643	0.92[CEU][hapmap]
rs6837359	0.96[CEU][hapmap]
rs6847124	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs71600251	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7672134	0.96[CEU][hapmap];0.90[CHB][hapmap]
rs7678323	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs9760870	0.86[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	nsv529623	chr4:98501338-99460166	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	esv2754250	chr4:99094922-99527122	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1004181	chr4:99208152-99529576	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99431200-99443600	Weak transcription	Fetal Brain Male	brain
2	chr4:99433000-99443200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr4:99434400-99443800	Weak transcription	Aorta	Aorta
4	chr4:99436600-99443600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr4:99436600-99446400	Weak transcription	Left Ventricle	heart
6	chr4:99437200-99443400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr4:99438000-99442600	Weak transcription	Dnd41	blood
8	chr4:99438400-99443200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr4:99438800-99443400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr4:99438800-99452000	Enhancers	Fetal Heart	heart
11	chr4:99439000-99442600	Weak transcription	HMEC	breast
12	chr4:99439000-99442800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr4:99439000-99443200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr4:99439200-99442600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr4:99439200-99442600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr4:99439200-99443200	Enhancers	NH-A	brain
17	chr4:99439400-99443200	Weak transcription	Colon Smooth Muscle	Colon
18	chr4:99439600-99445800	Enhancers	Ovary	ovary
19	chr4:99439800-99443800	Weak transcription	Fetal Brain Female	brain
20	chr4:99440000-99442800	Weak transcription	A549	lung
21	chr4:99440200-99442600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:99440200-99442600	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr4:99440200-99443400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr4:99440400-99442600	Weak transcription	Brain Substantia Nigra	brain
25	chr4:99440400-99442600	Weak transcription	HUVEC	blood vessel
26	chr4:99440400-99443400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr4:99440400-99443600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr4:99440400-99443800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr4:99440400-99458400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr4:99440600-99442600	Weak transcription	Brain Germinal Matrix	brain
31	chr4:99440800-99442600	Weak transcription	Brain Hippocampus Middle	brain
32	chr4:99440800-99442600	Weak transcription	Fetal Stomach	stomach
33	chr4:99440800-99443200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr4:99440800-99443200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr4:99440800-99443800	Weak transcription	Primary B cells from cord blood	blood
36	chr4:99441000-99443200	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr4:99441200-99442600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr4:99441200-99442600	Weak transcription	Brain Anterior Caudate	brain
39	chr4:99441200-99442600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr4:99441200-99443200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr4:99441200-99446400	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr4:99441400-99442600	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr4:99441400-99442600	Weak transcription	Fetal Thymus	thymus
44	chr4:99441400-99442600	Weak transcription	HSMM	muscle
45	chr4:99441400-99442600	Weak transcription	NHLF	lung
46	chr4:99441400-99442800	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr4:99441400-99443000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr4:99441600-99442600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr4:99441600-99442600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr4:99441600-99442600	Weak transcription	Muscle Satellite Cultured Cells	--

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