Variant report

Variant	rs6840610
Chromosome Location	chr4:99442044-99442045
allele	G/T
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:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10004753	0.90[YRI][hapmap];0.80[AFR][1000 genomes]
rs10489125	0.82[JPT][hapmap]
rs10516433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10516434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11945713	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13116201	0.91[YRI][hapmap]
rs1554849	1.00[JPT][hapmap]
rs17498778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17499015	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17564872	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17564998	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4699642	0.88[YRI][hapmap]
rs4699645	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4699654	0.82[JPT][hapmap]
rs56221164	0.95[ASN][1000 genomes]
rs59150136	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60026821	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60947018	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6532740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6532746	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6817773	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6830136	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6840239	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6846101	0.86[ASN][1000 genomes]
rs6853079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7666585	0.85[JPT][hapmap]
rs7667273	0.85[JPT][hapmap]
rs7667608	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7676155	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7688849	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7689116	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7689289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9761395	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[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	chr4:99439200-99442400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr4:99439200-99442600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr4:99439200-99442600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr4:99439200-99443200	Enhancers	NH-A	brain
18	chr4:99439400-99443200	Weak transcription	Colon Smooth Muscle	Colon
19	chr4:99439600-99445800	Enhancers	Ovary	ovary
20	chr4:99439800-99443800	Weak transcription	Fetal Brain Female	brain
21	chr4:99440000-99442200	Weak transcription	NHEK	skin
22	chr4:99440000-99442800	Weak transcription	A549	lung
23	chr4:99440200-99442400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr4:99440200-99442600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:99440200-99442600	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr4:99440200-99443400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr4:99440400-99442400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr4:99440400-99442600	Weak transcription	Brain Substantia Nigra	brain
29	chr4:99440400-99442600	Weak transcription	HUVEC	blood vessel
30	chr4:99440400-99443400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr4:99440400-99443600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr4:99440400-99443800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr4:99440400-99458400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr4:99440600-99442600	Weak transcription	Brain Germinal Matrix	brain
35	chr4:99440800-99442600	Weak transcription	Brain Hippocampus Middle	brain
36	chr4:99440800-99442600	Weak transcription	Fetal Stomach	stomach
37	chr4:99440800-99443200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr4:99440800-99443200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr4:99440800-99443800	Weak transcription	Primary B cells from cord blood	blood
40	chr4:99441000-99443200	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr4:99441200-99442600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr4:99441200-99442600	Weak transcription	Brain Anterior Caudate	brain
43	chr4:99441200-99442600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr4:99441200-99443200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr4:99441200-99446400	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr4:99441400-99442400	Weak transcription	Brain Cingulate Gyrus	brain
47	chr4:99441400-99442600	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr4:99441400-99442600	Weak transcription	Fetal Thymus	thymus
49	chr4:99441400-99442600	Weak transcription	HSMM	muscle
50	chr4:99441400-99442600	Weak transcription	NHLF	lung

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