Variant report

Variant	rs10798004
Chromosome Location	chr1:185265149-185265150
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:185256584..185258275-chr1:185263468..185265157,2	K562	blood:
2	chr1:185252978..185255340-chr1:185264252..185266302,2	K562	blood:
3	chr1:185255623..185257727-chr1:185264157..185265832,2	MCF-7	breast:
4	chr1:185260837..185263424-chr1:185264314..185267191,3	MCF-7	breast:
5	chr1:185123646..185125468-chr1:185264625..185266948,2	K562	blood:
6	chr1:185262982..185267023-chr1:185274757..185279030,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000116679	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10158623	0.82[EUR][1000 genomes]
rs10174	0.82[CEU][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs10218496	0.82[ASN][1000 genomes]
rs10752947	0.85[CEU][hapmap];0.82[TSI][hapmap]
rs10798002	0.82[EUR][1000 genomes]
rs10798003	0.84[ASW][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.83[JPT][hapmap];0.81[MKK][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10798006	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10911700	0.92[ASW][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.83[JPT][hapmap];0.97[LWK][hapmap];0.93[MKK][hapmap];0.82[TSI][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10911702	0.82[CEU][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs10911704	0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs10911706	0.85[ASN][1000 genomes]
rs10911707	0.93[CEU][hapmap];0.84[GIH][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs10911708	0.84[EUR][1000 genomes]
rs12026391	0.82[CEU][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs12096987	0.87[CHB][hapmap];0.81[ASN][1000 genomes]
rs12119471	0.83[ASN][1000 genomes]
rs12127840	0.83[ASN][1000 genomes]
rs12135172	0.87[CHB][hapmap];0.81[CHD][hapmap];0.83[ASN][1000 genomes]
rs12135769	0.84[ASW][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];0.88[TSI][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12136040	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1336753	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs17641003	0.86[EUR][1000 genomes]
rs1889976	0.92[ASW][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.83[JPT][hapmap];0.97[LWK][hapmap];0.96[MKK][hapmap];0.82[TSI][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2095610	0.93[ASN][1000 genomes]
rs2152707	0.85[EUR][1000 genomes]
rs2281416	0.93[CEU][hapmap];0.92[EUR][1000 genomes]
rs2295212	0.85[ASN][1000 genomes]
rs2378909	0.87[EUR][1000 genomes]
rs2378910	0.82[EUR][1000 genomes]
rs2383269	0.82[ASN][1000 genomes]
rs34611062	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57977436	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6424975	0.91[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs6666742	0.87[CHB][hapmap];0.82[CHD][hapmap];0.82[ASN][1000 genomes]
rs6682891	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6685627	0.82[EUR][1000 genomes]
rs6687774	0.93[CEU][hapmap];0.80[GIH][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs7123	0.96[CEU][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes]
rs726567	0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs7537341	1.00[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7539575	1.00[CHB][hapmap];0.83[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7539658	0.87[CHB][hapmap];0.82[CHD][hapmap];0.82[ASN][1000 genomes]
rs7542721	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7550599	0.82[ASN][1000 genomes]
rs883753	0.82[EUR][1000 genomes]
rs997283	0.92[EUR][1000 genomes]
rs9988622	0.85[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	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS 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	69 gene(s)	inside rSNPs	diseases
3	nsv548398	chr1:185136458-186003094	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10798004	RNF2	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:185218800-185269400	Weak transcription	Pancreas	Pancrea
2	chr1:185235400-185265400	Weak transcription	Brain Substantia Nigra	brain
3	chr1:185236600-185265600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:185240000-185265800	Weak transcription	Fetal Lung	lung
5	chr1:185240200-185267200	Weak transcription	Gastric	stomach
6	chr1:185240400-185268800	Weak transcription	Aorta	Aorta
7	chr1:185240800-185273000	Weak transcription	Spleen	Spleen
8	chr1:185245400-185268800	Weak transcription	Esophagus	oesophagus
9	chr1:185245800-185268400	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr1:185245800-185273000	Weak transcription	Right Ventricle	heart
11	chr1:185246800-185265600	Weak transcription	NHLF	lung
12	chr1:185247600-185267800	Weak transcription	Fetal Stomach	stomach
13	chr1:185248200-185266800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr1:185248800-185265200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr1:185249200-185265800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr1:185250200-185265400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:185250400-185265600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:185251200-185265600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr1:185251200-185266400	Weak transcription	Stomach Smooth Muscle	stomach
20	chr1:185252000-185266000	Weak transcription	Thymus	Thymus
21	chr1:185254200-185265600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr1:185254400-185266600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr1:185254400-185267800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:185254600-185266400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:185255000-185268200	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr1:185255200-185265600	Weak transcription	Psoas Muscle	Psoas
27	chr1:185257000-185266000	Weak transcription	Ovary	ovary
28	chr1:185258200-185266000	Weak transcription	Fetal Heart	heart
29	chr1:185258600-185265400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr1:185258600-185266800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr1:185258800-185265600	Weak transcription	Fetal Brain Male	brain
32	chr1:185260600-185265200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr1:185260800-185275200	Weak transcription	Small Intestine	intestine
34	chr1:185261200-185267800	Weak transcription	Fetal Intestine Small	intestine
35	chr1:185261400-185278800	Strong transcription	HUVEC	blood vessel
36	chr1:185261600-185265200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr1:185261800-185278800	Strong transcription	Fetal Brain Female	brain
38	chr1:185262000-185265200	Strong transcription	Fetal Muscle Leg	muscle
39	chr1:185262000-185265600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr1:185262000-185279000	Strong transcription	HSMMtube	muscle
41	chr1:185262000-185279400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr1:185262000-185279800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:185262000-185280400	Strong transcription	Placenta	Placenta
44	chr1:185262000-185280800	Strong transcription	HMEC	breast
45	chr1:185262000-185281000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr1:185262000-185281600	Strong transcription	Fetal Thymus	thymus
47	chr1:185262000-185281800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:185262000-185281800	Strong transcription	HSMM	muscle
49	chr1:185262200-185265400	Weak transcription	Brain Angular Gyrus	brain
50	chr1:185262200-185265600	Weak transcription	Primary B cells from peripheral blood	blood

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