Variant report

Variant	rs1598856
Chromosome Location	chr4:103446115-103446116
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:103439093..103441146-chr4:103445747..103447716,2	MCF-7	breast:
2	chr4:103421826..103424740-chr4:103443696..103446881,3	K562	blood:
3	chr4:103442501..103444375-chr4:103444794..103447284,2	K562	blood:
4	chr4:103441543..103444001-chr4:103444588..103447284,2	K562	blood:
5	chr4:103444323..103446252-chr4:103457244..103458889,2	K562	blood:

Variant related genes	Relation type
ENSG00000260651	Chromatin interaction
ENSG00000109320	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1054029	0.82[JPT][hapmap]
rs1585213	0.84[CHD][hapmap]
rs1585214	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1599961	0.84[CHD][hapmap]
rs17032705	0.84[CHD][hapmap]
rs17033015	0.91[CEU][hapmap];0.90[JPT][hapmap]
rs179195	0.81[JPT][hapmap]
rs227361	0.81[JPT][hapmap]
rs228614	0.81[JPT][hapmap]
rs228617	0.81[JPT][hapmap]
rs228619	0.81[JPT][hapmap]
rs230510	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs230530	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap]
rs3774932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3774968	0.96[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap]
rs434644	0.85[JPT][hapmap]
rs747559	0.84[CHD][hapmap]
rs93059	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap]
rs980455	0.84[CHD][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	nsv830020	chr4:103387343-103581284	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1003490	chr4:103391483-103521772	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1004030	chr4:103419352-103504042	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv537203	chr4:103419352-103504042	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1598856	RG9MTD2	cis	cerebellum	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103425200-103456400	Weak transcription	Osteobl	bone
2	chr4:103425600-103448400	Weak transcription	Fetal Thymus	thymus
3	chr4:103426000-103452600	Weak transcription	NH-A	brain
4	chr4:103426000-103456400	Weak transcription	NHDF-Ad	bronchial
5	chr4:103426400-103450000	Weak transcription	HMEC	breast
6	chr4:103426400-103452600	Weak transcription	HSMMtube	muscle
7	chr4:103426400-103460800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr4:103428000-103449200	Weak transcription	Fetal Kidney	kidney
9	chr4:103429200-103446200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr4:103431800-103447000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr4:103433200-103466000	Weak transcription	Hela-S3	cervix
12	chr4:103434000-103446800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr4:103436000-103448600	Weak transcription	HUVEC	blood vessel
14	chr4:103438000-103448200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr4:103438200-103448200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr4:103438400-103446800	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr4:103439800-103448400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr4:103440000-103459600	Weak transcription	Fetal Muscle Leg	muscle
19	chr4:103440000-103460600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr4:103440000-103466200	Weak transcription	Aorta	Aorta
21	chr4:103440000-103484800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr4:103440200-103451000	Weak transcription	Duodenum Mucosa	Duodenum
23	chr4:103440200-103460600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr4:103440200-103473200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr4:103440200-103478600	Weak transcription	Right Ventricle	heart
26	chr4:103440200-103488200	Weak transcription	Gastric	stomach
27	chr4:103441000-103448800	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr4:103441200-103448800	Weak transcription	Adipose Nuclei	Adipose
29	chr4:103441400-103464200	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr4:103441400-103469400	Weak transcription	Ovary	ovary
31	chr4:103441400-103482000	Weak transcription	Spleen	Spleen
32	chr4:103442400-103446400	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr4:103442400-103459600	Weak transcription	Fetal Stomach	stomach
34	chr4:103443000-103449200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr4:103443000-103455400	Weak transcription	HSMM	muscle
36	chr4:103443200-103449400	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr4:103443200-103474200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr4:103443200-103496000	Weak transcription	A549	lung
39	chr4:103443400-103455400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr4:103443600-103446800	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr4:103443600-103450000	Weak transcription	NHEK	skin
42	chr4:103443800-103456800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr4:103444000-103459600	Weak transcription	Fetal Intestine Small	intestine
44	chr4:103444200-103449000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr4:103444400-103470600	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr4:103444600-103448800	Weak transcription	Liver	Liver
47	chr4:103444600-103456000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr4:103444800-103448200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr4:103444800-103449000	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr4:103444800-103458600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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